diff --git a/RELEASE_NOTES b/RELEASE_NOTES index b32dbc5a765..2d0e7fe80c1 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,8 +3,46 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 8,831 easyconfig files, for 1,437 different software packages, -27 different (compiler) toolchains, 13 software bundles and 1 meta-package. +The latest version of easybuild-easyconfig provides 8,983 easyconfig files, for 1,461 different software packages, +30 different (compiler) toolchains, 13 software bundles and 1 meta-package. + +v3.6.1 (May 28th 2018) +---------------------- + +bugfix/update release +- added easyconfigs for new toolchains fosscuda/2018a (#6363) and giolfc/2017b (#5799) +- added example easyconfig files for 24 new software packages: + - BAGEL (#6332), Bottleneck (#6334), cisTEM (#6370), cftime (#6337), dotNET-Core-Runtime (#6345), ecCodes (#6235), + feh (#6300), Graphene (#5043), gffread (#6306), HOME (#6227), HiCExplorer (#6342), ICU (#6371), Imlib2 (#6300), + KmerGenie (#5929), libgeotiff (#6262), NetPIPE (#6062), Pandoc (#6247), Pisces (#6347), Proteinortho (#6333), + pyshp (#6364), SIMPLE (#6019), STIR (#6349), SimpleElastix (#6114), wxWidgets (#6370) +- added additional easyconfigs for various supported software packages, including: + - Boost 1.67.0, ESMF 7.1.0r, GATK 4.0.4.0, GCC 8.1.0, GROMACS 2018, OpenBLAS 0.3.0, PETSc 3.9.1, PGI 18.4, + TensorFlow 1.8.0, WIEN2k 17.1 +- minor enhancements, including: + - add py_expression_eval extension to (recent) Python 2.7.14 & 3.6.4 easyconfigs (#6285) + - add README for Java with information on downloading source tarball (#6294) + - add several extensions to Perl 5.26.1 easyconfigs, incl Dist::Zilla & dependencies (#6297) + - also include archive URLs for Bioconductor 3.6 (#6311) + - add README.md file for installing icc/ifort (#6317) +- various bug fixes, including: + - consistently specify 'intel-mkl' component in recent Intel MKL easyconfigs (#6234) + - add pkg-config as build dependency to libdrm (#6243) + - add pkg-config build dep to most recent libdrm easyconfigs (#6244) + - fix checksum for foreign extension in R 3.4.3 and R 3.4.4 easyconfigs (#6245) + - fix installation of Libint 2.4.2 by building with -std=c++11 (#6251) + - fix source spec for networkx 2.1 extension in scikit-image easyconfig (#6254) + - avoid that Nipype downloads dependencies for included extensions (#6261, #6263) + - consistently include patch for FLTK 1.3.4 (#6265) + - fix Perl shebang in MCL v14.137 scripts (#6269) + - add patch to build particular source file of matrixStats extension in R 3.4.4 easyconfig with -O1 to work around ICE in Skylake systems (#6278) + - add pkg-config build dependency to FFmpeg >= 3.3.1 (#6291) + - change back checksum for libdap 3.19.1 (#6305) + - add patch for Automake 1.15 to fix issue with recent Perl versions (#6358) + - fix ``glog`` causing intel error in Intel compilers on Intel Skylake (#6360) + - include ICU as dependency in recent R easyconfigs (v3.4.3 & v3.4.4) (#6371) + - fix checksum for RSEM 1.3.0 after sneaky re-release (#6379) + v3.6.0 (April 26th 2018) ------------------------ diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2017b.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2017b.eb new file mode 100644 index 00000000000..10ff1403b09 --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2017b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = '2.7.7' + +homepage = 'http://www.antlr2.org/' +description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) + is a language tool that provides a framework for constructing recognizers, + compilers, and translators from grammatical descriptions containing + Java, C#, C++, or Python actions.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['http://www.antlr2.org/download/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_includes.patch'] +checksums = [ + '853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9', # antlr-2.7.7.tar.gz + 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch +] + +dependencies = [('Java', '1.8.0_152', '', True)] + +configopts = '--disable-examples --disable-csharp --disable-python' + +sanity_check_paths = { + 'files': ['bin/antlr', 'bin/antlr-config'], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.7.2.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.7.2.eb index d0bdf5ce33d..65f245a0e26 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.7.2.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.8.4.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.8.4.eb index f0fe1e048a3..4b142d958d4 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.8.4.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'GCC', 'version': '4.8.4'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.2.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.2.eb index 7c92b98f676..24172c0f5dd 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.2.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.3-2.25.eb index f9456e27809..743a381147c 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.3-2.25.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.3.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.3.eb index 93877b0da86..32c7fbcf199 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.3.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'GCC', 'version': '4.9.3'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-5.2.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-5.2.0.eb index 21217b92b30..718168348f8 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-5.2.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-5.2.0.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'GCC', 'version': '5.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-5.4.0-2.26.eb index 1850bd252a8..f5004492dc8 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-5.4.0-2.26.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.2.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.2.eb index 38adcdbcb6a..d469fdb58f5 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.2.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'GCCcore', 'version': '4.9.2'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.3.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.3.eb index 3b56561e8de..18e77ac4ce8 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.3.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'GCCcore', 'version': '4.9.3'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] builddependencies = [('binutils', '2.25')] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.3.0.eb index 3835b3463d5..9d0d0b21a79 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.3.0.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'GCCcore', 'version': '5.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb index ff70a116e5f..3ee3bf9adf7 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.1.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.1.0.eb index 945983f162e..1b4be92da39 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.1.0.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'GCCcore', 'version': '6.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.2.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.2.0.eb index 89b19119869..c8c1c5b5d60 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.2.0.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'GCCcore', 'version': '6.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb index ef15fb72721..e447b6af5a2 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.2-2.25.eb index e58e17b276e..03b5657f4b5 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.2-2.25.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.3-2.25.eb index be935f87520..c65543b9790 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.3-2.25.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-5.1.0-2.25.eb index 5fa0b4cce0a..323f886bfcf 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-5.1.0-2.25.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-5.1.0-2.25.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'GNU', 'version': '5.1.0-2.25'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-fix-brace.patch b/easybuild/easyconfigs/a/Automake/Automake-1.15-fix-brace.patch new file mode 100644 index 00000000000..2c0ab6a857f --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-fix-brace.patch @@ -0,0 +1,19 @@ +Without this change, Perl 5.22 complains "Unescaped left brace in +regex is deprecated" and this is planned to become a hard error in +Perl 5.26. See: +http://search.cpan.org/dist/perl-5.22.0/pod/perldelta.pod#A_literal_%22{%22_should_now_be_escaped_in_a_pattern +* bin/automake.in (substitute_ac_subst_variables): Escape left brace. + +Backported from: +http://git.savannah.gnu.org/cgit/automake.git/commit/?id=13f00eb4493c217269b76614759e452d8302955e +Original author: Paul Eggert +--- a/bin/automake.in ++++ b/bin/automake.in +@@ -3878,7 +3878,7 @@ + sub substitute_ac_subst_variables + { + my ($text) = @_; +- $text =~ s/\${([^ \t=:+{}]+)}/substitute_ac_subst_variables_worker ($1)/ge; ++ $text =~ s/\$\{([^ \t=:+{}]+)\}/substitute_ac_subst_variables_worker ($1)/ge; + return $text; + } diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015a.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015a.eb index 71f728a244e..b313af871b3 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015a.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015a.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'foss', 'version': '2015a'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015b.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015b.eb index 8105a92a8d1..061e58a9a97 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015b.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015b.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'foss', 'version': '2015b'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016.04.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016.04.eb index 44615809054..7fbe3e7cd0e 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016.04.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016.04.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'foss', 'version': '2016.04'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016a.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016a.eb index ac34f15c490..07f19446a0d 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016a.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016a.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016b.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016b.eb index 1d42fcae7cf..598c6830ed7 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016b.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016b.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-gimkl-2.11.5.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-gimkl-2.11.5.eb index 693d3ee2b73..e4852831eee 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-gimkl-2.11.5.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.3.0.eb index 17832f07cde..60a8de85b22 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.3.0.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.5.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.5.0.eb index 79380a10313..ec0fed20347 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.5.0.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015a.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015a.eb index a5d90a232c7..77899c30738 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015a.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015a.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://ftp.gnu.org/gnu/automake'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015b.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015b.eb index 52bb62ffcc5..dbf655ee93d 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015b.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015b.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016.02-GCC-4.9.eb index 8f5f433315a..857f26b667f 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016.02-GCC-4.9.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016a.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016a.eb index 477fa282f97..78b29ba2168 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016a.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016a.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016b.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016b.eb index d561b8ba8c8..c4cf1841997 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016b.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016b.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.07.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.07.eb index 290f8e7c44d..01fd0f1d9b3 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.07.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'iomkl', 'version': '2016.07'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb index 30cc36477f2..56720c5a31c 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -22,7 +22,11 @@ toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924'] +patches = ['Automake-%(version)s-fix-brace.patch'] +checksums = [ + '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924', # automake-1.15.tar.gz + '9f72b339934d546ba8f8486d3ca601601a298963b66a20474245df524acaf0d7', # Automake-1.15-fix-brace.patch +] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-gimkl-2017a.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-gimkl-2017a.eb new file mode 100644 index 00000000000..3e0b385eba5 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-gimkl-2017a.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/BAGEL/BAGEL-1.1.1-intel-2016b.eb b/easybuild/easyconfigs/b/BAGEL/BAGEL-1.1.1-intel-2016b.eb new file mode 100644 index 00000000000..106ddc1b85f --- /dev/null +++ b/easybuild/easyconfigs/b/BAGEL/BAGEL-1.1.1-intel-2016b.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'BAGEL' +version = '1.1.1' + +homepage = "http://www.nubakery.org" +description = """BAGEL (Brilliantly Advanced General Electronic-structure Library) +is a parallel electronic-structure program.""" + +# Note: A compiler bug(?) in template deduction prevents newer versions of icpc to compile this software. +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/nubakery/bagel/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['60d46496c25d18698acf67f39ca7150d0c6daf49944a8e47cf0c10a0e31d245f'] + +builddependencies = [ + ('Autotools', '20150215'), +] + +dependencies = [ + ('Boost', '1.61.0'), + ('libxc', '2.2.3'), +] + +# Hack, because bagel-v1.1.1 uses outdated filenames: +preconfigopts = 'sed -i "s|-gcc-mt||g" configure.ac && ' +preconfigopts += './autogen.sh && ' +preconfigopts += 'CXXFLAGS="$CXXFLAGS -DNDEBUG" ' +configopts = ' --with-boost=$BOOST_ROOT --with-mpi=intel --enable-mkl --with-libxc ' + +sanity_check_paths = { + 'files': ['bin/BAGEL', 'lib/libbagel.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.7.1-foss-2018a.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.7.1-foss-2018a.eb new file mode 100644 index 00000000000..21378991c02 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.7.1-foss-2018a.eb @@ -0,0 +1,54 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.7.1' + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2018a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +patches = ['%(name)s-%(version)s_boost_backport.patch'] +checksums = [ + '10a78d3007413a6d4c983d2acbf03ef84b622b82bd9a59c6bd9fbdde9d0298ca', # ncbi-blast-2.7.1+-src.tar.gz + 'e3f9c80ea242dd58759f18919467d9af0e1bec5c01142d130ee479c18cecc654', # BLAST+-2.7.1_boost_backport.patch +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('PCRE', '8.41'), + ('Boost', '1.66.0'), + ('GMP', '6.1.2'), + ('libpng', '1.6.34'), + ('libjpeg-turbo', '1.5.3'), + ('LMDB', '0.9.21'), +] + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 --with-pcre=$EBROOTPCRE " +configopts += "--with-boost=$EBROOTBOOST --with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.7.1-intel-2018a.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.7.1-intel-2018a.eb new file mode 100644 index 00000000000..4cbc3a8e893 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.7.1-intel-2018a.eb @@ -0,0 +1,61 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.7.1' + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'cstd': 'c++14', 'usempi': True} + +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +patches = [ + 'BLAST+-2.2.30_ictce-fixes.patch', + '%(name)s-%(version)s_boost_backport.patch', +] +checksums = [ + '10a78d3007413a6d4c983d2acbf03ef84b622b82bd9a59c6bd9fbdde9d0298ca', # ncbi-blast-2.7.1+-src.tar.gz + '8892e8bc0b1020a2e8616594da364c63009839d0d2dc6faf4bae9c44122a78be', # BLAST+-2.2.30_ictce-fixes.patch + 'e3f9c80ea242dd58759f18919467d9af0e1bec5c01142d130ee479c18cecc654', # BLAST+-2.7.1_boost_backport.patch +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('PCRE', '8.41'), + ('Boost', '1.66.0'), + ('GMP', '6.1.2'), + ('libpng', '1.6.34'), + ('libjpeg-turbo', '1.5.3'), + ('LMDB', '0.9.21'), +] + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 --with-pcre=$EBROOTPCRE " +configopts += "--with-boost=$EBROOTBOOST --with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +# configure script uses -openmp with Intel compilers, which is no longer valid (-fopenmp is more generic than -qopenmp) +configopts = "OPENMP_FLAGS='-fopenmp'" + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.7.1_boost_backport.patch b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.7.1_boost_backport.patch new file mode 100644 index 00000000000..aa56d10d314 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.7.1_boost_backport.patch @@ -0,0 +1,157 @@ +backporting Boost 1.66 support from BLAST+ 2.8 alpha +author: Albert Bogdanowicz +diff -Nru ncbi-blast-2.7.1+-src.orig/c++/src/corelib/teamcity_boost.cpp ncbi-blast-2.7.1+-src/c++/src/corelib/teamcity_boost.cpp +--- ncbi-blast-2.7.1+-src.orig/c++/src/corelib/teamcity_boost.cpp 2017-05-03 13:23:39.000000000 +0200 ++++ ncbi-blast-2.7.1+-src/c++/src/corelib/teamcity_boost.cpp 2018-04-26 11:17:07.787295628 +0200 +@@ -12,7 +12,7 @@ + * See the License for the specific language governing permissions and + * limitations under the License. + * +- * $Id: teamcity_boost.cpp 534856 2017-05-03 11:23:39Z ivanov $ ++ * $Revision: 549230 $ + */ + + #include +@@ -83,6 +83,17 @@ + virtual void entry_context_start(std::ostream&, boost::unit_test::log_level); + virtual void log_entry_context(std::ostream&, boost::unit_test::const_string); + virtual void entry_context_finish(std::ostream&); ++ ++#if BOOST_VERSION >= 106500 ++ // Since v1.65.0 the log level is passed to the formatters for the contexts ++ // See boostorg/test.git:fcb302b66ea09c25f0682588d22fbfdf59eac0f7 ++ void log_entry_context(std::ostream& os, boost::unit_test::log_level, boost::unit_test::const_string ctx) { ++ log_entry_context(os, ctx); ++ } ++ void entry_context_finish(std::ostream& os, boost::unit_test::log_level) { ++ entry_context_finish(os); ++ } ++#endif + }; + + // Fake fixture to register formatter +@@ -90,14 +101,17 @@ + TeamcityFormatterRegistrar() { + if (underTeamcity()) { + boost::unit_test::unit_test_log.set_formatter(new TeamcityBoostLogFormatter()); +- boost::unit_test::unit_test_log.set_threshold_level +- (RTCFG(but::log_level, LOG_LEVEL, log_level)); ++ boost::unit_test::unit_test_log.set_threshold_level(boost::unit_test::log_test_units); + } + } + }; + + BOOST_GLOBAL_FIXTURE(TeamcityFormatterRegistrar); + ++// Dummy method used to keep object file in case of static library linking ++// See README.md and https://github.com/JetBrains/teamcity-cpp/pull/19 ++void TeamcityGlobalFixture() {} ++ + // Formatter implementation + static std::string toString(boost::unit_test::const_string bstr) { + std::stringstream ss; +diff -Nru ncbi-blast-2.7.1+-src.orig/c++/src/corelib/test_boost.cpp ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp +--- ncbi-blast-2.7.1+-src.orig/c++/src/corelib/test_boost.cpp 2017-04-27 13:53:27.000000000 +0200 ++++ ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp 2018-04-26 11:16:58.863187073 +0200 +@@ -1,4 +1,4 @@ +-/* $Id: test_boost.cpp 534439 2017-04-27 11:53:27Z ivanov $ ++/* $Id: test_boost.cpp 549229 2017-10-23 14:47:48Z ucko $ + * =========================================================================== + * + * PUBLIC DOMAIN NOTICE +@@ -95,8 +95,15 @@ + + #if BOOST_VERSION >= 106000 + # define attr_value utils::attr_value +-# define RTCFG(type, new_name, old_name) \ +- but::runtime_config::get(but::runtime_config::new_name) ++# if BOOST_VERSION >= 106400 ++ // Everything old is new again, apparently... ++# define RTCFG(type, new_name, old_name) \ ++ but::runtime_config::get(but::runtime_config::btrt_##old_name) ++# define CONFIGURED_FILTERS RTCFG(std::vector, _, run_filters) ++# else ++# define RTCFG(type, new_name, old_name) \ ++ but::runtime_config::get(but::runtime_config::new_name) ++# endif + #else + # define RTCFG(type, new_name, old_name) but::runtime_config::old_name() + # if BOOST_VERSION >= 105900 +@@ -112,8 +119,10 @@ + # endif + #endif + +-#define CONFIGURED_FILTERS \ ++#ifndef CONFIGURED_FILTERS ++ #define CONFIGURED_FILTERS \ + RTCFG(std::vector, RUN_FILTERS, test_to_run) ++#endif + + #ifdef NCBI_COMPILER_MSVC + # pragma warning(pop) +@@ -278,11 +287,19 @@ + virtual + void entry_context_start(ostream& ostr, but::log_level l); + ++# if BOOST_VERSION >= 106500 ++ virtual ++ void log_entry_context(ostream& os, but::log_level l, but::const_string v); ++ ++ virtual ++ void entry_context_finish(ostream& os, but::log_level l); ++# else + virtual + void log_entry_context(ostream& ostr, but::const_string value); + + virtual + void entry_context_finish (ostream& ostr); ++# endif + #endif + + private: +@@ -1456,7 +1473,7 @@ + but::test_unit* tu = GetTestUnit(test_name); + if (tu) { + list koef_lst; +- NStr::Split(reg_value, ";", koef_lst, NStr::fSplit_NoMergeDelims); ++ NStr::Split(reg_value, ";", koef_lst); + ITERATE(list, it_koef, koef_lst) { + CTempString koef_str, koef_cond; + if (NStr::SplitInTwo(*it_koef, ":", koef_str, koef_cond)) { +@@ -2124,6 +2141,19 @@ + m_Upper->entry_context_start(ostr, l); + } + ++# if BOOST_VERSION >= 106500 ++void CNcbiBoostLogger::log_entry_context(ostream& ostr, ++ but::log_level l, ++ but::const_string value) ++{ ++ m_Upper->log_entry_context(ostr, l, value); ++} ++ ++void CNcbiBoostLogger::entry_context_finish(ostream& ostr, but::log_level l) ++{ ++ m_Upper->entry_context_finish(ostr, l); ++} ++# else + void CNcbiBoostLogger::log_entry_context(ostream& ostr, + but::const_string value) + { +@@ -2134,6 +2164,7 @@ + { + m_Upper->entry_context_finish(ostr); + } ++# endif + #endif + + void +@@ -2316,7 +2347,7 @@ + + if ( + #if BOOST_VERSION >= 106000 +- runtime_config::get( runtime_config::RESULT_CODE ) ++ RTCFG(bool, RESULT_CODE, result_code) + #else + !runtime_config::no_result_code() + #endif diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.12.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.12.0-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..ba628d6babe --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.12.0-GCCcore-6.4.0.eb @@ -0,0 +1,17 @@ +name = 'Bazel' +version = '0.12.0' + +homepage = 'http://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-dist.zip'] +checksums = ['3b3e7dc76d145046fdc78db7cac9a82bc8939d3b291e53a7ce85315feb827754'] + +builddependencies = [('binutils', '2.28')] +dependencies = [('Java', '1.8.0_162', '', True)] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2018a.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2018a.eb new file mode 100644 index 00000000000..ec636463b08 --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2018a.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'BerkeleyGW' +version = '1.2.0' + +homepage = 'http://www.berkeleygw.org' +description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle + properties and the optical responses of a large variety of materials from bulk periodic crystals to + nanostructures such as slabs, wires and molecules.""" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['http://www.berkeleygw.org/releases/'] # requires registration +sources = ['BGW-%(version)s.tar.gz'] +patches = ['BerkeleyGW-%(version)s_fix_intent.patch'] +checksums = [ + '1305dc8587af666fe437bc2561a9106b2b0bcdbe91980b8f1ae7bbd491ce1e25', # BGW-1.2.0.tar.gz + '7bd3cc229693a1bd5fe6547f55046bee68c8c50f29f8ca6945f443b04ce2ca38', # BerkeleyGW-1.2.0_fix_intent.patch +] + +skipsteps = ['configure'] + +prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk && ' + +buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" ' +buildopts += 'FOPTS="$FFLAGS" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' +buildopts += 'FCPP="cpp -C -P -ffreestanding" C_LINK="$MPICXX" C_OPTS="$CFLAGS" MKLPATH="$MKLROOT" ' +buildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' +buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" ' + +# "all-flavors" cleans and compiles everything again +preinstallopts = 'sed -i "s/install: all-flavors/install: all/" Makefile && ' + +installopts = 'INSTDIR=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/' + prog + '.' + flavor + '.x' + for prog in ['epsilon', 'sigma', 'kernel', 'absorption', 'nonlinearoptics'] + for flavor in ['real', 'cplx']], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0_fix_intent.patch b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0_fix_intent.patch new file mode 100644 index 00000000000..8b2dee63c41 --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0_fix_intent.patch @@ -0,0 +1,103 @@ +* fix intent of pointer arguments that are already associated on subroutine entry +* see https://groups.google.com/a/berkeleygw.org/forum/#!topic/help/hL_jRdFfVLo +author: Miguel Dias Costa (National University of Singapore) +--- Sigma/mtxel_cor.f90.orig 2018-03-14 08:50:52.920787000 +0800 ++++ Sigma/mtxel_cor.f90 2018-03-14 08:51:28.489516380 +0800 +@@ -78,11 +78,11 @@ + !> (ncoulch) Uninitialized unless freq_dep=0 .or. exact_ch=1 + SCALAR, pointer, intent(in) :: aqsch(:) + !> (sig%ntband) Uninitialized in FF calculations +- SCALAR, pointer, intent(out) :: acht_n1(:) ++ SCALAR, pointer, intent(inout) :: acht_n1(:) + !> (3 or sig%nfreqeval) Uninitialized unless freq_dep=1 +- SCALAR, pointer, intent(out) :: asxt(:), acht(:) ++ SCALAR, pointer, intent(inout) :: asxt(:), acht(:) + ! FHJ: static remainder, resolved over bands +- SCALAR, pointer, intent(out) :: achtcor_n1(:) ++ SCALAR, pointer, intent(inout) :: achtcor_n1(:) + SCALAR, intent(out) :: achtcor + SCALAR, intent(out) :: asigt_imag + integer, intent(in) :: nspin +@@ -92,9 +92,9 @@ + integer, intent(in) :: ngpown + !> The following pointers are uninitialized unless we are running the complex version + complex(DPC), pointer, intent(in) :: epsR(:,:,:),epsA(:,:,:) !< (neps,ngpown,sig%nFreq) +- complex(DPC), pointer, intent(out) :: achtD_n1(:) !< (sig%ntband) +- complex(DPC), pointer, intent(out) :: asxtDyn(:), achtDyn(:), achtDyn_cor(:), ach2tDyn(:) !< (sig%nfreqeval) +- complex(DPC), pointer, intent(out) :: achtDyn_corb(:) !< (sig%nfreqeval) ++ complex(DPC), pointer, intent(inout) :: achtD_n1(:) !< (sig%ntband) ++ complex(DPC), pointer, intent(inout) :: asxtDyn(:), achtDyn(:), achtDyn_cor(:), ach2tDyn(:) !< (sig%nfreqeval) ++ complex(DPC), pointer, intent(inout) :: achtDyn_corb(:) !< (sig%nfreqeval) + integer, intent(in) :: icalc + + SCALAR, allocatable :: epstemp(:), aqsntemp(:,:),aqsmtemp(:,:) +--- ./Common/wfn_rho_vxc_io_inc.f90.orig 2018-04-26 12:48:49.469693000 +0800 ++++ ./Common/wfn_rho_vxc_io_inc.f90 2018-04-26 12:48:38.654492000 +0800 +@@ -8,6 +8,7 @@ + #ifdef READ + #define READ_WRITE(x) read ## x + #define INTENT out ++ #define POINTER_INTENT inout + #define FLAVOR_INTENT inout + #else + #define READ_WRITE(x) write ## x +@@ -68,13 +69,13 @@ + !! lattice vectors, metric tensor in reciprocal space (in a.u., bvec in units of blat) + integer, intent(INTENT) :: mtrx(3, 3, 48) !< symmetry matrix + real(DP), intent(INTENT) :: tnp(3, 48) !< fractional translation +- integer, pointer, intent(INTENT) :: atyp(:) !< atomic species +- real(DP), pointer, intent(INTENT) :: apos(:,:) !< atomic positions (in units of alat) +- integer, pointer, intent(INTENT) :: ngk(:) !< number of G-vectors for each k-pt, ngk(nk) +- real(DP), pointer, intent(INTENT) :: kw(:), kpt(:, :) !< k-weight, kw(nk); k-coord, kpt(3, nk) in crystal coords +- integer, pointer, intent(INTENT) :: ifmin(:, :), ifmax(:, :) !< lowest and highest occupied band, ifmin/max(nk, ns) +- real(DP), pointer, intent(INTENT) :: energies(:, :, :) !< energies(nbands, nk, ns) in Ry +- real(DP), pointer, intent(INTENT) :: occupations(:, :, :) !< occupations(nbands, nk, ns) between 0 and 1 ++ integer, pointer, intent(POINTER_INTENT) :: atyp(:) !< atomic species ++ real(DP), pointer, intent(POINTER_INTENT) :: apos(:,:) !< atomic positions (in units of alat) ++ integer, pointer, intent(POINTER_INTENT) :: ngk(:) !< number of G-vectors for each k-pt, ngk(nk) ++ real(DP), pointer, intent(POINTER_INTENT) :: kw(:), kpt(:, :) !< k-weight, kw(nk); k-coord, kpt(3, nk) in crystal coords ++ integer, pointer, intent(POINTER_INTENT) :: ifmin(:, :), ifmax(:, :) !< lowest and highest occupied band, ifmin/max(nk, ns) ++ real(DP), pointer, intent(POINTER_INTENT) :: energies(:, :, :) !< energies(nbands, nk, ns) in Ry ++ real(DP), pointer, intent(POINTER_INTENT) :: occupations(:, :, :) !< occupations(nbands, nk, ns) between 0 and 1 + integer, optional, intent(INTENT) :: nspinor !< 2 if doing a two-component spinor calculation; 1 if not present + logical, optional, intent(in) :: warn !< if false, suppresses warnings about inversion symmetries etc. + logical, optional, intent(in) :: dont_warn_kgrid !< if true, validity of kgrid read will not be checked. +@@ -475,7 +476,7 @@ + TEMP_SCALAR, intent(INTENT) :: data(:, :) !< (ng_bound, ns) + #endif + integer, optional, intent(INTENT) :: nrecord !< data/gvectors will be distributed among this many records +- integer, optional, pointer, intent(INTENT) :: ng_record(:) !< number of gvectors in each record ++ integer, optional, pointer, intent(POINTER_INTENT) :: ng_record(:) !< number of gvectors in each record + !! must be provided for write if nrecord > 1 + logical, optional, intent(in) :: bcast !< whether to do MPI_Bcast of what is read + integer, optional, intent(in) :: gindex(:) !< map of order in file to order in gvec +@@ -671,13 +672,13 @@ + real(DP), intent(INTENT) :: recvol, blat, bvec(3, 3), bdot(3, 3) !< cell volume, lattice constant, + integer, intent(INTENT) :: mtrx(3, 3, 48) !< symmetry matrix + real(DP), intent(INTENT) :: tnp(3, 48) !< fractional translation +- integer, pointer, intent(INTENT) :: atyp(:) !< atomic species +- real(DP), pointer, intent(INTENT) :: apos(:,:) !< atomic positions (in units of alat) +- integer, pointer, intent(INTENT) :: ngk(:) !< number of G-vectors for each k-pt, ngk(nk) +- real(DP), pointer, intent(INTENT) :: kw(:), kpt(:, :) !< k-weight, kw(nk); k-coord, kpt(3, nk) in crystal coords +- integer, pointer, intent(INTENT) :: ifmin(:, :), ifmax(:, :) !< lowest and highest occupied band, ifmin/max(nk, ns) +- real(DP), pointer, intent(INTENT) :: energies(:, :, :) !< energies(nbands, nk, ns) in Ry +- real(DP), pointer, intent(INTENT) :: occupations(:, :, :) !< occupations(nbands, nk, ns) between 0 and 1 ++ integer, pointer, intent(POINTER_INTENT) :: atyp(:) !< atomic species ++ real(DP), pointer, intent(POINTER_INTENT) :: apos(:,:) !< atomic positions (in units of alat) ++ integer, pointer, intent(POINTER_INTENT) :: ngk(:) !< number of G-vectors for each k-pt, ngk(nk) ++ real(DP), pointer, intent(POINTER_INTENT) :: kw(:), kpt(:, :) !< k-weight, kw(nk); k-coord, kpt(3, nk) in crystal coords ++ integer, pointer, intent(POINTER_INTENT) :: ifmin(:, :), ifmax(:, :) !< lowest and highest occupied band, ifmin/max(nk, ns) ++ real(DP), pointer, intent(POINTER_INTENT) :: energies(:, :, :) !< energies(nbands, nk, ns) in Ry ++ real(DP), pointer, intent(POINTER_INTENT) :: occupations(:, :, :) !< occupations(nbands, nk, ns) between 0 and 1 + integer, intent(INTENT) :: nspinor !< 2 if doing a two-component spinor calculation; 1 if not present + logical, optional, intent(in) :: warn !< if false, suppresses warnings about inversion symmetries etc. + character(len=32), optional, intent(out) :: sdate, stime !< if read, result from file is returned; if write, current is returned +@@ -749,7 +750,7 @@ + TEMP_SCALAR, intent(INTENT) :: data(:, :) !< (ng_bound, ns) + #endif + integer, optional, intent(INTENT) :: nrecord !< data/gvectors will be distributed among this many records +- integer, optional, pointer, intent(INTENT) :: ng_record(:) !< number of gvectors in each record ++ integer, optional, pointer, intent(POINTER_INTENT) :: ng_record(:) !< number of gvectors in each record + logical, optional, intent(in) :: bcast !< whether to do MPI_Bcast of what is read + integer, optional, intent(in) :: gindex(:) !< map of order in file to order in gvec + logical, optional, intent(in) :: dont_read !< if true, records will just be skipped; only for unformatted diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.2-intel-2018a-Perl-5.26.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.2-intel-2018a-Perl-5.26.1.eb new file mode 100644 index 00000000000..a6973af6ad1 --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.2-intel-2018a-Perl-5.26.1.eb @@ -0,0 +1,30 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Fred Hutchinson Cancer Research Center + +easyblock = 'PerlModule' + +name = 'BioPerl' +version = '1.7.2' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://www.bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['release-%s.zip' % version.replace('.', '-')] +checksums = ['cbed57a76751c724dce0706df144a3bbed8fa1b1c2d079783067ce58809952aa'] + +dependencies = [ + ('Perl', '5.26.1'), + ('XML-LibXML', '2.0132', versionsuffix), +] + +options = {'modulename': 'Bio::Perl'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-8.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-8.1.0.eb new file mode 100644 index 00000000000..d6b304185cb --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-8.1.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '8.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b67fd2daae7a64b5ba862c66c07c1addb9e6b1b05c5f2049392cfd8a2172952e'] + +builddependencies = [ + ('M4', '1.4.18'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.30', '', True), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.67.0-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/b/Boost/Boost-1.67.0-foss-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..ed2efa5e5d0 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.67.0-foss-2018a-Python-2.7.14.eb @@ -0,0 +1,24 @@ +name = 'Boost' +version = '1.67.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2018a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['8aa4e330c870ef50a896634c931adf468b21f8a69b77007e45c444151229f665'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('Python', '2.7.14'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.2.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.2.1-intel-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..0956110f550 --- /dev/null +++ b/easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.2.1-intel-2018a-Python-3.6.4.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'Bottleneck' +version = '1.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://kwgoodman.github.io/bottleneck-doc' +description = "Fast NumPy array functions written in C" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6efcde5f830aed64feafca0359b51db0e184c72af8ba6675b4a99f263922eb36'] + +dependencies = [('Python', '3.6.4')] + +download_dep_fail = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/b/behave/behave-1.2.6-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/b/behave/behave-1.2.6-intel-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..3a42621268a --- /dev/null +++ b/easybuild/easyconfigs/b/behave/behave-1.2.6-intel-2018a-Python-3.6.4.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'behave' +version = '1.2.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pythonhosted.org/behave' +description = """behave: Behavior-driven development (or BDD) is an +agile software development technique that encourages collaboration +between developers, QA and non-technical or business participants in a +software project.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b9662327aa53294c1351b0a9c369093ccec1d21026f050c3bd9b3e5cccf81a86'] + +dependencies = [('Python', '3.6.4')] + +sanity_check_paths = { + 'files': ['bin/behave'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb new file mode 100644 index 00000000000..f01e9f9437e --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb @@ -0,0 +1,22 @@ +name = 'binutils' +version = '2.30' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '8.1.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] +checksums = ['8c3850195d1c093d290a716e20ebcaa72eda32abf5e3d8611154b39cff79e9ea'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.11'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-intel-2018a.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-intel-2018a.eb new file mode 100644 index 00000000000..0037242748d --- /dev/null +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-intel-2018a.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'CD-HIT' +version = '4.6.8' + +homepage = 'http://weizhong-lab.ucsd.edu/cd-hit/' +description = """ CD-HIT is a very widely used program for clustering and + comparing protein or nucleotide sequences.""" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/weizhongli/cdhit/archive/'] +sources = ['V%(version)s.tar.gz'] +checksums = ['37d685e4aa849314401805fe4d4db707e1d06070368475e313d6f3cb8fb65949'] + +# make sure compilation flags are passed down (e.g. to enable OpenMP) +buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' + +# put here the list of generated executables when compiling +list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] + +# this is the real EasyBuild line to copy all the executables and perl scripts to "bin" +files_to_copy = [(list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] + +postinstallcmds = ["sed -i 's@#!/usr/bin/perl@/usr/bin/env perl@' %(installdir)s/bin/*.pl"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in list_of_executables], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..27070c69ab0 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,37 @@ +name = 'CGAL' +version = '4.11.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['fb152fc30f007e5911922913f8dc38e0bb969b534373ca0fbe85b4d872300e8b'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '2.7.14'), + ('Boost', '1.66.0'), + ('MPFR', '4.0.1'), + ('GMP', '6.1.2'), + ('libGLU', '9.0.0'), + ('Qt5', '5.10.1'), +] + +builddependencies = [ + ('CMake', '3.10.2'), + ('Eigen', '3.3.4', '', True), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.11.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.11.1-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..526960767cd --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.11.1-GCCcore-6.4.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.11.1' + +homepage = 'http://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['57bebc6ca4d1d42c6385249d148d9216087e0fda57a47dc5c858790a70217d0c'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('ncurses', '6.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.0g'), +] + +osdependencies = [ + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/Caffe/Caffe-1.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/Caffe/Caffe-1.0-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..5b0aee96f38 --- /dev/null +++ b/easybuild/easyconfigs/c/Caffe/Caffe-1.0-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,59 @@ +# -*- mode: python; -*- +# EasyBuild reciPY for Caffe as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2017 UL HPC +# Authors:: UL HPC Team +# License:: MIT/GPL +# +easyblock = 'CMakeMake' + +name = 'Caffe' +version = '1.0' + +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/BVLC/caffe' +description = """ +Caffe is a deep learning framework made with expression, speed, +and modularity in mind. It is developed by the Berkeley Vision +and Learning Center (BVLC) and community contributors. +""" + +toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/BVLC/caffe/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['71d3c9eb8a183150f965a465824d01fe82826c22505f7aa314f700ace03fa77f'] + +builddependencies = [ + ('CMake', '3.9.1'), +] + +# See http://caffe.berkeleyvision.org/installation.html +dependencies = [ + ('Python', '2.7.14'), + ('Boost', '1.66.0', '-Python-%(pyver)s'), + ('protobuf', '3.4.0'), + ('protobuf-python', '3.4.0', '-Python-%(pyver)s'), + ('glog', '0.3.5'), + ('gflags', '2.2.1'), + ('HDF5', '1.8.20'), + ('LMDB', '0.9.21'), + ('LevelDB', '1.18'), + ('snappy', '1.1.7'), + ('scikit-image', '0.13.1', '-Python-%(pyver)s'), +] + +configopts = '-DBLAS=mkl -DUSE_OPENCV=0 -DUSE_MKL2017_AS_DEFAULT_ENGINE=1 -DCPU_ONLY=1 ' + +modextrapaths = {'PYTHONPATH': ['python']} + +sanity_check_paths = { + 'files': ['bin/caffe', 'include/caffe/proto/caffe.pb.h', 'lib64/libproto.a', 'lib64/libcaffe.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = [('python', "-c 'import caffe'")] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..4dc482510d7 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.59.0' + +homepage = 'http://curl.haxx.se' + +description = """ + libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, + LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. + libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP + form based upload, proxies, cookies, user+password authentication (Basic, + Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling + and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['https://curl.haxx.se/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['099d9c32dc7b8958ca592597c9fabccdf4c08cfb7c114ff1afbbc4c6f13c9e9e'] + +osdependencies = [ + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.0e') + ('zlib', '1.2.11'), +] + +configopts = '--with-zlib=$EBROOTZLIB' +# configopts += '--with-ssl=$EBROOTOPENSSL' + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cftime/cftime-1.0.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/c/cftime/cftime-1.0.0-intel-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..1c620391792 --- /dev/null +++ b/easybuild/easyconfigs/c/cftime/cftime-1.0.0-intel-2018a-Python-3.6.4.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'cftime' +version = '1.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Unidata/cftime' +description = """Time-handling functionality from netcdf4-python""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['https://github.com/Unidata/cftime/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['2ec37b5e5126b70a3328a40fd903ff6303e232ec3bb2c5d7272580f6cd50e0d6'] + +dependencies = [ + ('Python', '3.6.4'), + ('cURL', '7.58.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/c/cftime/cftime-1.0.0b1-foss-2017b-Python-3.6.2.eb b/easybuild/easyconfigs/c/cftime/cftime-1.0.0b1-foss-2017b-Python-3.6.2.eb new file mode 100644 index 00000000000..5bd658127d2 --- /dev/null +++ b/easybuild/easyconfigs/c/cftime/cftime-1.0.0b1-foss-2017b-Python-3.6.2.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'cftime' +version = '1.0.0b1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Unidata/cftime' +description = """Time-handling functionality from netcdf4-python""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['https://github.com/Unidata/cftime/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['edba7681ac2641a3e44e4f4679c2b55d545b4eee74f0e3f1e3649a8944a14970'] + +dependencies = [ + ('Python', '3.6.2'), + ('cURL', '7.56.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/c/cisTEM/cisTEM-1.0.0-beta-foss-2018a.eb b/easybuild/easyconfigs/c/cisTEM/cisTEM-1.0.0-beta-foss-2018a.eb new file mode 100644 index 00000000000..a370635d7d1 --- /dev/null +++ b/easybuild/easyconfigs/c/cisTEM/cisTEM-1.0.0-beta-foss-2018a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'cisTEM' +version = '1.0.0-beta' + +homepage = 'https://cistem.org/' +description = """ cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes + and obtain high-resolution 3D reconstructions from them. """ + +toolchain = {'name': 'foss', 'version': '2018a'} +toolchainopts = {'pic': True} + +source_urls = ['https://cistem.org/system/tdf/upload3'] +sources = [{'filename': SOURCELOWER_TAR_GZ, 'download_filename': '%(namelower)s-%(version)s-source-code.tar.gz?file=1'}] + +patches = ['cisTEM-1.0.0-beta_fix_wxWidgets_version.patch'] +checksums = [ + 'c62068f53d0a269ffa1bfff34641597d3795989a930686437fba9eed7a991af6', # cistem-1.0.0-beta.tar.gz + '91dc72879e105c80f136188ad8c4db197e901974df96c79a337955eaea849688', # cisTEM-1.0.0-beta_fix_wxWidgets_version.patch +] + +dependencies = [ + ('Mesa', '17.3.6'), + ('libGLU', '9.0.0'), + ('wxWidgets', '3.0.3'), +] + +sanity_check_paths = { + 'files': ['bin/cisTEM'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/cisTEM/cisTEM-1.0.0-beta_fix_wxWidgets_version.patch b/easybuild/easyconfigs/c/cisTEM/cisTEM-1.0.0-beta_fix_wxWidgets_version.patch new file mode 100644 index 00000000000..a2fb87e26f0 --- /dev/null +++ b/easybuild/easyconfigs/c/cisTEM/cisTEM-1.0.0-beta_fix_wxWidgets_version.patch @@ -0,0 +1,14 @@ +Use wxWidgets version 3.0.3 instead of 3.0.2 (version 3.0.2 reports as 3.0.1) +author: Sam Moors, Vrije Universiteit Brussel (VUB) +diff -ur cistem-1.0.0-beta.orig/configure cistem-1.0.0-beta/configure +--- cistem-1.0.0-beta.orig/configure 2017-12-03 02:10:52.000000000 +0100 ++++ cistem-1.0.0-beta/configure 2018-05-24 13:41:28.749291371 +0200 +@@ -15184,7 +15184,7 @@ + + # Verify minimus requires + vers=`echo $wxversion | $AWK 'BEGIN { FS = "."; } { printf "% d", ($1 * 1000 + $2) * 1000 + $3;}'` +-if test -n "$vers" && test "$vers" -eq 3000002; then ++if test -n "$vers" && test "$vers" -eq 3000003; then + WX_CPPFLAGS="`$WXCONFIG --cppflags`" + WX_CXXFLAGS="`$WXCONFIG --cxxflags | sed -e 's/-fno-exceptions//'`" + WX_LIBS="`$WXCONFIG --libs richtext,std,aui`" diff --git a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.9.22-intel-2018a.eb b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.9.22-intel-2018a.eb new file mode 100644 index 00000000000..b874568d9c4 --- /dev/null +++ b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.9.22-intel-2018a.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'DIAMOND' +version = '0.9.22' + +homepage = 'https://github.com/bbuchfink/diamond' +description = """DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance + analysis of big sequence data.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['https://github.com/bbuchfink/diamond/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['35e518cfa0ac2fbc57e422d380bdb5123c6335742dd7965b76c34c95f241b729'] + +builddependencies = [('CMake', '3.10.2')] +dependencies = [('zlib', '1.2.11')] + +sanity_check_paths = { + 'files': ['bin/diamond'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-2.0.7-GCCcore-6.4.0.eb b/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-2.0.7-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..d32d2d32f11 --- /dev/null +++ b/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-2.0.7-GCCcore-6.4.0.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +# note: only works on recent OSs, required sufficiently recent glibc (2.14 or newer) +name = 'dotNET-Core-Runtime' +version = '2.0.7' + +homepage = 'https://www.microsoft.com/net/' +description = """.NET is a free, cross-platform, open source developer platform for building many different types + of applications.""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['https://download.microsoft.com/download/A/9/F/A9F8872C-48B2-41DB-8AAD-D5908D988592/'] +sources = ['dotnet-runtime-%(version)s-linux-x64.tar.gz'] +checksums = ['680ea40a1fafb7a6f93897df70077b64f0081b7d9b0f1358f5897ffd949d6b71'] + +dependencies = [('libunwind', '1.2.1')] + +sanity_check_paths = { + 'files': ['dotnet'], + 'dirs': ['shared/Microsoft.NETCore.App/%(version)s'], +} + +modextrapaths = {'PATH': ['']} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-foss-2018a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-foss-2018a.eb new file mode 100644 index 00000000000..a737290934c --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-foss-2018a.eb @@ -0,0 +1,51 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'ELPA' +version = '2015.02.002' + +homepage = 'http://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications .""" + +toolchain = {'name': 'foss', 'version': '2018a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c26201de0c226cb659350b048d74f555c316df3029a0eba7a95ff9903dfac872'] + +builddependencies = [ + ('Autotools', '20170619'), +] + +preconfigopts = 'autoreconf && ' + +common_configopts = 'LIBS="$LIBSCALAPACK" ' + +configopts = [ + common_configopts + '--enable-openmp ', + common_configopts, # Default version last, so we can get the normal config.h/config-f90.h installed afterwards. +] + +buildopts = ' V=1 ' + +postinstallcmds = [ + 'cp config.h config-f90.h %(installdir)s/share/doc/elpa/examples', +] + +sanity_check_paths = { + 'files': ['lib/libelpa.a', 'lib/libelpa.%s' % SHLIB_EXT, 'lib/libelpa_openmp.a', + 'lib/libelpa_openmp.%s' % SHLIB_EXT, 'share/doc/elpa/examples/config.h', + 'share/doc/elpa/examples/config-f90.h'], + 'dirs': ['bin', 'include/elpa-%(version)s/elpa', 'include/elpa-%(version)s/modules', 'lib/pkgconfig'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-gimkl-2017a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-gimkl-2017a.eb new file mode 100644 index 00000000000..e30e5498dd9 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-gimkl-2017a.eb @@ -0,0 +1,53 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'ELPA' +version = '2015.02.002' + +homepage = 'http://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications .""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c26201de0c226cb659350b048d74f555c316df3029a0eba7a95ff9903dfac872'] + +builddependencies = [ + ('Autotools', '20150215'), +] + +preconfigopts = 'autoreconf && ' + +common_configopts = 'FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" ' +common_configopts += 'LDFLAGS="$LDFLAGS $LIBS" ' +common_configopts += 'LIBS="$LIBSCALAPACK" ' + +configopts = [ + common_configopts + '--enable-openmp ', + common_configopts, # Default version last, so we can get the normal config.h/config-f90.h installed afterwards. +] + +buildopts = ' V=1 ' + +postinstallcmds = [ + 'cp config.h config-f90.h %(installdir)s/share/doc/elpa/examples', +] + +sanity_check_paths = { + 'files': ['lib/libelpa.a', 'lib/libelpa.%s' % SHLIB_EXT, 'lib/libelpa_openmp.a', + 'lib/libelpa_openmp.%s' % SHLIB_EXT, 'share/doc/elpa/examples/config.h', + 'share/doc/elpa/examples/config-f90.h'], + 'dirs': ['bin', 'include/elpa-%(version)s/elpa', 'include/elpa-%(version)s/modules', 'lib/pkgconfig'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-intel-2018a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-intel-2018a.eb new file mode 100644 index 00000000000..7d16ec6abb5 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-intel-2018a.eb @@ -0,0 +1,52 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'ELPA' +version = '2015.02.002' + +homepage = 'http://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications .""" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c26201de0c226cb659350b048d74f555c316df3029a0eba7a95ff9903dfac872'] + +builddependencies = [ + ('Autotools', '20170619'), +] + +preconfigopts = 'autoreconf && ' + +common_configopts = 'FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 -nofor_main $FCFLAGS" ' +common_configopts += 'LIBS="$LIBSCALAPACK" ' + +configopts = [ + common_configopts + '--enable-openmp ', + common_configopts, # Default version last, so we can get the normal config.h/config-f90.h installed afterwards. +] + +buildopts = ' V=1 ' + +postinstallcmds = [ + 'cp config.h config-f90.h %(installdir)s/share/doc/elpa/examples', +] + +sanity_check_paths = { + 'files': ['lib/libelpa.a', 'lib/libelpa.%s' % SHLIB_EXT, 'lib/libelpa_openmp.a', + 'lib/libelpa_openmp.%s' % SHLIB_EXT, 'share/doc/elpa/examples/config.h', + 'share/doc/elpa/examples/config-f90.h'], + 'dirs': ['bin', 'include/elpa-%(version)s/elpa', 'include/elpa-%(version)s/modules', 'lib/pkgconfig'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-7.1.0r-intel-2018a.eb b/easybuild/easyconfigs/e/ESMF/ESMF-7.1.0r-intel-2018a.eb new file mode 100644 index 00000000000..13cdd3cbb33 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-7.1.0r-intel-2018a.eb @@ -0,0 +1,31 @@ +name = 'ESMF' +version = '7.1.0r' + +homepage = 'http://sourceforge.net/projects/esmf' +description = """The Earth System Modeling Framework (ESMF) is software for building and coupling weather, + climate, and related models.""" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s_src.tar.gz' % '_'.join(version.split('.'))] +patches = ['ESMF-6.1.1_libopts.patch'] +checksums = [ + 'ae9a5edb8d40ae97a35cbd4bd00b77061f995c77c43d36334dbb95c18b00a889', # esmf_7_1_0r_src.tar.gz + '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4', # ESMF-6.1.1_libopts.patch +] + +dependencies = [ + ('netCDF', '4.6.0'), + ('netCDF-Fortran', '4.4.4'), + ('netCDF-C++4', '4.3.0'), +] + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.6.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.6.0.eb new file mode 100644 index 00000000000..3b52bbec57c --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.6.0.eb @@ -0,0 +1,45 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '3.6.0' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # vsc-install + 'https://files.pythonhosted.org/packages/5d/ca/1c41be2964be1355e15b4a88c7eef11c13c621220e27b69b2686c23cace2/', + # vsc-base + 'https://files.pythonhosted.org/packages/f7/66/1ff7ecc4a93ba37e063f5bfbe395e95a547b1dec73b017c2724f4475a958/', + # easybuild-framework + 'https://files.pythonhosted.org/packages/eb/cd/013ef3982b1699abf729f76517cb2d7c9df04432abb5b8dde56ccc7ef250/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/91/92/43412bb7d2959fabfd111faf01547240fcd149b8a973b7565198ca7373d5/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/f3/f3/9fcd8e62df069770eae6b69233d17c68d3a60170e445580a0566f09d98ff/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.32.tar.gz', + 'vsc-base-2.5.8.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + '56f614328451d924aeb9ece0b53552b1f3c247d723e741794aa201762af61b64', # vsc-install-0.10.32.tar.gz + '7fcd300f842edf4baade7d0b7a3b462ca7dfb2a411a7532694a90127c6646ee2', # vsc-base-2.5.8.tar.gz + 'ff75fd81c956bc0ab6592dd728ae32f11e6769fdbdbe69ec692f969f336348c3', # easybuild-framework-3.6.0.tar.gz + '8314dca3dc9e3c068650ee41fa51a23b38093e40957d01112733d5f1a5322ed4', # easybuild-easyblocks-3.6.0.tar.gz + '758d09ed38ed96e3bbf956cb1ceb2aa9fc7cfae269ab58e375f50c56f97dac71', # easybuild-easyconfigs-3.6.0.tar.gz +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.7.3-intel-2018a.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.7.3-intel-2018a.eb new file mode 100644 index 00000000000..d332d2fd433 --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.7.3-intel-2018a.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.7.3' + +homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home' +description = """ecCodes is a package developed by ECMWF which provides an application programming interface and + a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, + WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['https://software.ecmwf.int/wiki/download/attachments/45757960/'] +sources = ['eccodes-%(version)s-Source.tar.gz'] +checksums = ['6fab143dbb34604bb2e04d10143855c0906b00411c1713fd7ff5c35519b871db'] + +builddependencies = [('CMake', '3.10.2')] +dependencies = [ + ('netCDF', '4.6.0'), + ('JasPer', '2.0.14'), +] + +separate_build_dir = True + +configopts = "-DENABLE_NETCDF=ON -DENABLE_JPG=ON" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bufr_copy', 'bufr_dump', 'bufr_filter', 'bufr_ls', + 'codes_count', 'codes_info', 'codes_split_file', + 'grib_copy', 'grib_dump', 'grib_filter', 'grib_ls']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gimpic-2017b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gimpic-2017b.eb new file mode 100644 index 00000000000..179d1a6abe7 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gimpic-2017b.eb @@ -0,0 +1,17 @@ +name = 'FFTW' +version = '3.3.6' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gimpic', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s-pl2.tar.gz'] +checksums = ['a5de35c5c824a78a058ca54278c706cdf3d4abba1c56b63531c2cb05f5d57da2'] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.7-gimkl-2017a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.7-gimkl-2017a.eb new file mode 100644 index 00000000000..f1ada231923 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.7-gimkl-2017a.eb @@ -0,0 +1,17 @@ +name = 'FFTW' +version = '3.3.7' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3b609b7feba5230e8f6dd8d245ddbefac324c5a6ae4186947670d9ac2cd25573'] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.7-gmpich-2017.08.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.7-gmpich-2017.08.eb new file mode 100644 index 00000000000..6c55a8fb9ff --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.7-gmpich-2017.08.eb @@ -0,0 +1,17 @@ +name = 'FFTW' +version = '3.3.7' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gmpich', 'version': '2017.08'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3b609b7feba5230e8f6dd8d245ddbefac324c5a6ae4186947670d9ac2cd25573'] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.1-foss-2016b.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.1-foss-2016b.eb index 374f64671c2..9d0056b657e 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.1-foss-2016b.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.1-foss-2016b.eb @@ -8,8 +8,11 @@ description = """A complete, cross-platform solution to record, convert and stre toolchain = {'name': 'foss', 'version': '2016b'} -sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ffmpeg.org/releases/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['fcb2cd7b77fcb66a00abccd5a04e34342a02cab9f89626f28cf1abca715b6730'] + +builddependencies = [('pkg-config', '0.29.1')] dependencies = [ ('NASM', '2.12.02'), diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.4-intel-2017a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.4-intel-2017a.eb index 4be73253c54..d48dae9b24b 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.4-intel-2017a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.4-intel-2017a.eb @@ -12,6 +12,8 @@ source_urls = ['http://ffmpeg.org/releases/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['5ef5e9276c311c74ab2e9d301c2d7ee10e1f2cbd758c6f13d6cb9514dffbac7e'] +builddependencies = [('pkg-config', '0.29.1')] + dependencies = [ ('NASM', '2.13.01'), ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.4-GCCcore-6.4.0.eb index f0225f93377..6764a147edf 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.4-GCCcore-6.4.0.eb @@ -8,12 +8,14 @@ description = """A complete, cross-platform solution to record, convert and stre toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ffmpeg.org/releases/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['5d8911fe6017d00c98a359d7c8e7818e48f2c0cc2c9086a986ea8cb4d478c85e'] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain ('binutils', '2.28'), + ('pkg-config', '0.29.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.4.1-foss-2017b.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.4.1-foss-2017b.eb index 110ab078bcd..1501682b6f8 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.4.1-foss-2017b.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.4.1-foss-2017b.eb @@ -12,6 +12,8 @@ source_urls = ['http://ffmpeg.org/releases/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['f3443e20154a590ab8a9eef7bc951e8731425efc75b44ff4bee31d8a7a574a2c'] +builddependencies = [('pkg-config', '0.29.2')] + dependencies = [ ('NASM', '2.13.01'), ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.4.1-intel-2017b.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.4.1-intel-2017b.eb index 258377f44d5..905124807cf 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.4.1-intel-2017b.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.4.1-intel-2017b.eb @@ -12,6 +12,8 @@ source_urls = ['http://ffmpeg.org/releases/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['f3443e20154a590ab8a9eef7bc951e8731425efc75b44ff4bee31d8a7a574a2c'] +builddependencies = [('pkg-config', '0.29.2')] + dependencies = [ ('NASM', '2.13.01'), ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.4.2-foss-2018a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.4.2-foss-2018a.eb index d6f6cadeb0d..85604dad7aa 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.4.2-foss-2018a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.4.2-foss-2018a.eb @@ -12,6 +12,8 @@ source_urls = ['http://ffmpeg.org/releases/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['eb0370bf223809b9ebb359fed5318f826ac038ce77933b3afd55ab1a0a21785a'] +builddependencies = [('pkg-config', '0.29.2')] + dependencies = [ ('NASM', '2.13.03'), ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.4.2-intel-2018a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.4.2-intel-2018a.eb index 1470a7c3062..3993f4708d2 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.4.2-intel-2018a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.4.2-intel-2018a.eb @@ -12,6 +12,8 @@ source_urls = ['http://ffmpeg.org/releases/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['eb0370bf223809b9ebb359fed5318f826ac038ce77933b3afd55ab1a0a21785a'] +builddependencies = [('pkg-config', '0.29.2')] + dependencies = [ ('NASM', '2.13.03'), ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-foss-2017b.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-foss-2017b.eb index c04ec512e46..4380a8b58e5 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-foss-2017b.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-foss-2017b.eb @@ -16,7 +16,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] sources = ['%(namelower)s-%(version)s-source.tar.gz'] -checksums = ['c8ab01c4e860d53e11d40dc28f98d2fe9c85aaf6dbb5af50fd6e66afec3dc58f'] +patches = ['FLTK-%(version)s_fix-LDFLAGS.patch'] +checksums = [ + 'c8ab01c4e860d53e11d40dc28f98d2fe9c85aaf6dbb5af50fd6e66afec3dc58f', # fltk-1.3.4-source.tar.gz + 'b9d39f6dce92fdb34a149f686a5d56e72912f94fd09c4958f3bb12770603da7d', # FLTK-1.3.4_fix-LDFLAGS.patch +] configopts = '--enable-shared --enable-threads --enable-xft' diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-intel-2017a.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-intel-2017a.eb index 95391e1838a..3f14952a569 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-intel-2017a.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-intel-2017a.eb @@ -16,6 +16,11 @@ toolchainopts = {'optarch': True, 'pic': True} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] +patches = ['FLTK-%(version)s_fix-LDFLAGS.patch'] +checksums = [ + 'c8ab01c4e860d53e11d40dc28f98d2fe9c85aaf6dbb5af50fd6e66afec3dc58f', # fltk-1.3.4-source.tar.gz + 'b9d39f6dce92fdb34a149f686a5d56e72912f94fd09c4958f3bb12770603da7d', # FLTK-1.3.4_fix-LDFLAGS.patch +] configopts = '--enable-shared --enable-threads --enable-xft' diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.10-intel-2018a.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.10-intel-2018a.eb new file mode 100644 index 00000000000..bb5c772d302 --- /dev/null +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.10-intel-2018a.eb @@ -0,0 +1,29 @@ +easyblock = 'CmdCp' + +name = 'FastTree' +version = '2.1.10' + +homepage = 'http://www.microbesonline.org/fasttree/' +description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide + or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of + time and memory. """ + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://www.microbesonline.org/fasttree/'] +sources = ['%(name)s-%(version)s.c'] +checksums = ['54cb89fc1728a974a59eae7a7ee6309cdd3cddda9a4c55b700a71219fc6e926d'] + +skipsteps = ['source'] + +cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] + +files_to_copy = [(['FastTree'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/FastTree'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/feh/feh-2.26-GCCcore-6.4.0.eb b/easybuild/easyconfigs/f/feh/feh-2.26-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..1dc964bc40e --- /dev/null +++ b/easybuild/easyconfigs/f/feh/feh-2.26-GCCcore-6.4.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'feh' +version = '2.26' + +homepage = 'https://feh.finalrewind.org/' +description = """ +feh is an X11 image viewer aimed mostly at console users. +Unlike most other viewers, it does not have a fancy GUI, but simply displays images. +It is controlled via commandline arguments and configurable key/mouse actions. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://feh.finalrewind.org'] +sources = [SOURCE_TAR_BZ2] +checksums = ['b1d6bfdd79060d864b8eff05b916153be04801998148620125e3ac31f99f6c86'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('cURL', '7.58.0'), + ('Imlib2', '1.5.1'), + ('X11', '20180131'), +] + +skipsteps = ['configure'] + +buildopts = 'PREFIX=%(installdir)s' +installopts = buildopts + +sanity_check_paths = { + 'files': ['bin/feh'], + 'dirs': ['share'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.1.0.eb new file mode 100644 index 00000000000..14894d3c3d5 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.1.0.eb @@ -0,0 +1,30 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'http://flex.sourceforge.net/' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.0.4'), + ('help2man', '1.47.6'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.30', '', True), +] + +dependencies = [ + ('M4', '1.4.18'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/fosscuda/fosscuda-2018a.eb b/easybuild/easyconfigs/f/fosscuda/fosscuda-2018a.eb new file mode 100644 index 00000000000..189e8d499b3 --- /dev/null +++ b/easybuild/easyconfigs/f/fosscuda/fosscuda-2018a.eb @@ -0,0 +1,34 @@ +easyblock = "Toolchain" + +name = 'fosscuda' +version = '2018a' + +homepage = '(none)' +description = """GCC based compiler toolchain __with CUDA support__, and including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '6.4.0-2.28' + +blaslib = 'OpenBLAS' +blasver = '0.2.20' +blas = '-%s-%s' % (blaslib, blasver) + +# toolchain used to build fosscuda dependencies +comp_mpi_tc_name = 'gompic' +comp_mpi_tc = (comp_mpi_tc_name, version) + +# compiler toolchain dependencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +dependencies = [ + ('GCC', gccver), # part of gompic + ('CUDA', '9.1.85', '', ('GCC', gccver)), # part of gompic + ('OpenMPI', '2.1.2', '', ('gcccuda', version)), # part of gompic + (blaslib, blasver, '', ('GCC', gccver)), + ('FFTW', '3.3.7', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', blas, comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.4.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.4.0-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..4a926a82dd9 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.4.0-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,48 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified by: Adam Huffman +# The Francis Crick Institute +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '4.0.4.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] +sources = ['gatk-%(version)s.zip'] +checksums = ['801bbb181c275cfabc96dc0cb21f3f901634cec11efde9ba9c8b91e2834feef4'] + +dependencies = [ + ('Python', '2.7.14'), + ('Java', '1.8.0_162', '', True), +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['gatk'], + 'dirs': [], +} +sanity_check_commands = ["gatk --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.4.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.4.0-intel-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..597a6f976c6 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.4.0-intel-2018a-Python-3.6.4.eb @@ -0,0 +1,48 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified by: Adam Huffman +# The Francis Crick Institute +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '4.0.4.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] +sources = ['gatk-%(version)s.zip'] +checksums = ['801bbb181c275cfabc96dc0cb21f3f901634cec11efde9ba9c8b91e2834feef4'] + +dependencies = [ + ('Python', '3.6.4'), + ('Java', '1.8.0_162', '', True), +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['gatk'], + 'dirs': [], +} +sanity_check_commands = ["gatk --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GCC/GCC-8.1.0-2.30.eb b/easybuild/easyconfigs/g/GCC/GCC-8.1.0-2.30.eb new file mode 100644 index 00000000000..9f586d06175 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-8.1.0-2.30.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '8.1.0' + +binutilsver = '2.30' +versionsuffix = '-%s' % binutilsver + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-8.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.1.0.eb new file mode 100644 index 00000000000..69b348f5d64 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.1.0.eb @@ -0,0 +1,53 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '8.1.0' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +mpfr_version = '4.0.1' + +source_urls = [ + 'http://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL +] +sources = [ + 'gcc-%(version)s.tar.gz', + 'gmp-6.1.2.tar.bz2', + 'mpfr-%s.tar.bz2' % mpfr_version, + 'mpc-1.1.0.tar.gz', + 'isl-0.19.tar.bz2', +] +patches = [ + 'GCCcore-6.2.0-fix-find-isl.patch', +] +checksums = [ + 'af300723841062db6ae24e38e61aaf4fbf3f6e5d9fd3bf60ebbdbf95db4e9f09', # gcc-8.1.0.tar.gz + '5275bb04f4863a13516b2f39392ac5e272f5e1bb8057b18aec1c9b79d73d8fb2', # gmp-6.1.2.tar.bz2 + 'a4d97610ba8579d380b384b225187c250ef88cfe1d5e7226b89519374209b86b', # mpfr-4.0.1.tar.bz2 + '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e', # mpc-1.1.0.tar.gz + 'd59726f34f7852a081fbd3defd1ab2136f174110fc2e0c8d10bb122173fa9ed8', # isl-0.19.tar.bz2 + '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch +] + +builddependencies = [ + ('M4', '1.4.18'), + ('binutils', '2.30'), + # a sufficiently recent GCC is required (needs to support -flto), so can't rely on system GCC + ('GCCcore', '6.4.0'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-foss-2018a-Python-3.6.4.eb index 3d5218d0786..2e8050c472a 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-foss-2018a-Python-3.6.4.eb @@ -32,12 +32,14 @@ dependencies = [ ('cURL', '7.58.0'), ('PCRE', '8.41'), ('PROJ', '5.0.0'), + ('libgeotiff', '1.4.2'), ] configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2018-05-11-intel-2018a.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2018-05-11-intel-2018a.eb new file mode 100644 index 00000000000..c6624daa90e --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2018-05-11-intel-2018a.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 2016-11-07 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'GMAP-GSNAP' +version = '2018-05-11' + +homepage = 'http://research-pub.gene.com/gmap/' +description = """GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences + GSNAP: Genomic Short-read Nucleotide Alignment Program""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['http://research-pub.gene.com/gmap/src/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b054cb538d1be40f9a71137263e716ace811fa62df3861cee3e22847b463b34a'] + +# with these deps you can use standard compressed files +# to support files in gobby format take a look at README for extra dependencies +# http://research-pub.gene.com/gmap/src/README +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), +] + +# you can change the MAX_READLENGTH for GSNAP with something like this. +# details in the README http://research-pub.gene.com/gmap/src/README +# configopts = 'MAX_READLENGTH=250' + +sanity_check_paths = { + 'files': ['bin/gmap', 'bin/gsnap'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018-foss-2018a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018-foss-2018a.eb new file mode 100644 index 00000000000..a3490bf32af --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018-foss-2018a.eb @@ -0,0 +1,22 @@ +name = 'GROMACS' +version = '2018' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. +This is CPU only build, containing both MPI and threadMPI builds. +""" + +toolchain = {'name': 'foss', 'version': '2018a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['deb5d0b749a52a0c6083367b5f50a99e08003208d81954fb49e7009e1b1fd0e9'] + +builddependencies = [ + ('CMake', '3.10.2'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..58a57b4d082 --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-6.4.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '9.23' + +homepage = 'http://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f65964807a3c97a2c0810d4b9806585367e73129e57ae33378cea18e07a1ed9b'] + +dependencies = [ + ('zlib', '1.2.11'), + ('libpng', '1.6.34'), + ('freetype', '2.9'), + ('libjpeg-turbo', '1.5.3'), + ('expat', '2.2.5'), + ('GLib', '2.54.3'), + ('cairo', '1.14.12'), + ('LibTIFF', '4.0.9'), +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.28'), +] + +# Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no && " +preconfigopts += 'export LIBS="$LIBS -lz" && ' + +configopts = "--with-system-libtiff --enable-dynamic" + +sanity_check_paths = { + 'files': ['bin/gs'], + 'dirs': ['lib/ghostscript', 'share/man'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/Graphene/Graphene-1.6.0-intel-2017a.eb b/easybuild/easyconfigs/g/Graphene/Graphene-1.6.0-intel-2017a.eb new file mode 100644 index 00000000000..125a9e28ee3 --- /dev/null +++ b/easybuild/easyconfigs/g/Graphene/Graphene-1.6.0-intel-2017a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Graphene' +version = '1.6.0' + +homepage = 'http://ebassi.github.io/graphene/' +description = "Graphene is a a thin layer of types for graphic libraries" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/ebassi/graphene/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['98970f859e452ce421b72726ca727fdf3ac27cb4804b62bfe520157fa46aa2fd'] + +builddependencies = [ + ('Autotools', '20150215'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.53.5', '-Python-3.6.1'), +] +dependencies = [ + ('GLib', '2.53.5'), +] + +preconfigopts = "./autogen.sh && " +configopts = "--enable-introspection=yes" + +sanity_check_paths = { + 'files': ['lib/libgraphene-1.0.%s' % SHLIB_EXT, 'share/gir-1.0/Graphene-1.0.gir'], + 'dirs': ['include/graphene-1.0', 'lib/pkgconfig'], +} + +modextrapaths = {'XDG_DATA_DIRS': 'share'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gffread/gffread-0.9.12-foss-2016b.eb b/easybuild/easyconfigs/g/gffread/gffread-0.9.12-foss-2016b.eb new file mode 100644 index 00000000000..6a42a350b15 --- /dev/null +++ b/easybuild/easyconfigs/g/gffread/gffread-0.9.12-foss-2016b.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'gffread' +version = '0.9.12' + +homepage = 'https://github.com/gpertea/%(name)s' +description = """GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and + more.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +github_account = 'gpertea' +source_urls = [ + GITHUB_SOURCE, + 'https://github.com/%(github_account)s/gclib/archive', +] +sources = [ + 'v%(version)s.tar.gz', + {'filename': 'gclib-20180215.tar.gz', 'download_filename': 'b790ac1.tar.gz'}, +] +checksums = [ + 'a059e7097a8355dd36f0bca0040735b32e520a587bb12eb0d6a734b57e983b91', + 'cc9abead10ebe15acea8512f398f0d5e065a2563b3e29260b282ad5e5d7e38bd', +] + +prebuildopts = "mv ../gclib-* ../gclib && " + +files_to_copy = ['%(name)s', 'LICENSE', 'README.md'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['%(name)s'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gimpic/gimpic-2017b.eb b/easybuild/easyconfigs/g/gimpic/gimpic-2017b.eb new file mode 100644 index 00000000000..82c8372145c --- /dev/null +++ b/easybuild/easyconfigs/g/gimpic/gimpic-2017b.eb @@ -0,0 +1,23 @@ +easyblock = "Toolchain" + +name = 'gimpic' +version = '2017b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, + including IntelMPI for MPI support with CUDA features enabled.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_ver = '6.4.0-2.28' +comp = (comp_name, comp_ver) + +# compiler toolchain dependencies +dependencies = [ + comp, # part of gcccuda + ('CUDA', '9.0.176', '', comp), # part of gcccuda + ('impi', '2017.3.196', '', ('gcccuda', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/giolfc/giolfc-2017b.eb b/easybuild/easyconfigs/g/giolfc/giolfc-2017b.eb new file mode 100644 index 00000000000..9cab8f58cfd --- /dev/null +++ b/easybuild/easyconfigs/g/giolfc/giolfc-2017b.eb @@ -0,0 +1,37 @@ +easyblock = "Toolchain" + +name = 'giolfc' +version = '2017b' + +homepage = '(none)' +description = """GCC based compiler toolchain __with CUDA support__, and including + IntelMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_ver = '6.4.0-2.28' +comp = (comp_name, comp_ver) + +# toolchain used to build goolfc dependencies +comp_mpi_tc_name = 'gimpic' +comp_mpi_tc_ver = version +comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) + +blaslib = 'OpenBLAS' +blasver = '0.2.20' +blas = '-%s-%s' % (blaslib, blasver) + +# compiler toolchain dependencies +# we need GCC and IntelMPI as explicit dependencies instead of gimpic toolchain +# because of toolchain preperation functions +dependencies = [ + comp, # part of gimpic + ('CUDA', '9.0.176', '', comp), # part of gimpic + ('impi', '2017.3.196', '', ('gcccuda', version)), + (blaslib, blasver, '', comp), + ('FFTW', '3.3.6', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', blas, comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/glog/glog-0.3.5-intel-2017a.eb b/easybuild/easyconfigs/g/glog/glog-0.3.5-intel-2017a.eb index a41d712cc48..8aa57a80c8b 100644 --- a/easybuild/easyconfigs/g/glog/glog-0.3.5-intel-2017a.eb +++ b/easybuild/easyconfigs/g/glog/glog-0.3.5-intel-2017a.eb @@ -18,7 +18,11 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['https://github.com/google/glog/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['7580e408a2c0b5a89ca214739978ce6ff480b5e7d8d7698a2aa92fadc484d1e0'] +patches = ['%(name)s-%(version)s_intel.patch'] +checksums = [ + '7580e408a2c0b5a89ca214739978ce6ff480b5e7d8d7698a2aa92fadc484d1e0', # v0.3.5.tar.gz + '1e923189adf15e1b09687a0d4be3adc733ff602b3b6a331a78e779707ac3239c', # glog-0.3.5_intel.patch +] sanity_check_paths = { 'files': ['include/glog/logging.h', 'include/glog/raw_logging.h', 'lib/libglog.a', 'lib/libglog.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/g/glog/glog-0.3.5-intel-2017b.eb b/easybuild/easyconfigs/g/glog/glog-0.3.5-intel-2017b.eb index 35f9f1d3ddc..5fbf35f9edd 100644 --- a/easybuild/easyconfigs/g/glog/glog-0.3.5-intel-2017b.eb +++ b/easybuild/easyconfigs/g/glog/glog-0.3.5-intel-2017b.eb @@ -18,7 +18,11 @@ toolchain = {'name': 'intel', 'version': '2017b'} source_urls = ['https://github.com/google/glog/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['7580e408a2c0b5a89ca214739978ce6ff480b5e7d8d7698a2aa92fadc484d1e0'] +patches = ['%(name)s-%(version)s_intel.patch'] +checksums = [ + '7580e408a2c0b5a89ca214739978ce6ff480b5e7d8d7698a2aa92fadc484d1e0', # v0.3.5.tar.gz + '1e923189adf15e1b09687a0d4be3adc733ff602b3b6a331a78e779707ac3239c', # glog-0.3.5_intel.patch +] sanity_check_paths = { 'files': ['include/glog/logging.h', 'include/glog/raw_logging.h', 'lib/libglog.a', 'lib/libglog.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/g/glog/glog-0.3.5_intel.patch b/easybuild/easyconfigs/g/glog/glog-0.3.5_intel.patch new file mode 100644 index 00000000000..e0a109880df --- /dev/null +++ b/easybuild/easyconfigs/g/glog/glog-0.3.5_intel.patch @@ -0,0 +1,13 @@ +# internal error on skylakes with intel/2017b compiler +# may 23rd 2018 by balazs hajgato (free university brussels - vub) +--- glog-0.3.5/Makefile.in.orig 2017-05-10 13:47:23.000000000 +0200 ++++ glog-0.3.5/Makefile.in 2018-02-26 10:52:51.153987941 +0100 +@@ -1209,7 +1209,7 @@ + @am__fastdepCXX_FALSE@ $(AM_V_CXX@am__nodep@)$(LIBTOOL) $(AM_V_lt) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libglog_la_CXXFLAGS) $(CXXFLAGS) -c -o src/libglog_la-symbolize.lo `test -f 'src/symbolize.cc' || echo '$(srcdir)/'`src/symbolize.cc + + src/libglog_la-signalhandler.lo: src/signalhandler.cc +-@am__fastdepCXX_TRUE@ $(AM_V_CXX)$(LIBTOOL) $(AM_V_lt) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libglog_la_CXXFLAGS) $(CXXFLAGS) -MT src/libglog_la-signalhandler.lo -MD -MP -MF src/$(DEPDIR)/libglog_la-signalhandler.Tpo -c -o src/libglog_la-signalhandler.lo `test -f 'src/signalhandler.cc' || echo '$(srcdir)/'`src/signalhandler.cc ++@am__fastdepCXX_TRUE@ $(AM_V_CXX)$(LIBTOOL) $(AM_V_lt) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libglog_la_CXXFLAGS) $(CXXFLAGS) -O1 -MT src/libglog_la-signalhandler.lo -MD -MP -MF src/$(DEPDIR)/libglog_la-signalhandler.Tpo -c -o src/libglog_la-signalhandler.lo `test -f 'src/signalhandler.cc' || echo '$(srcdir)/'`src/signalhandler.cc + @am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) src/$(DEPDIR)/libglog_la-signalhandler.Tpo src/$(DEPDIR)/libglog_la-signalhandler.Plo + @AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='src/signalhandler.cc' object='src/libglog_la-signalhandler.lo' libtool=yes @AMDEPBACKSLASH@ + @AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@ diff --git a/easybuild/easyconfigs/g/gmpolf/gmpolf-2017.10.eb b/easybuild/easyconfigs/g/gmpolf/gmpolf-2017.10.eb new file mode 100644 index 00000000000..138e8545765 --- /dev/null +++ b/easybuild/easyconfigs/g/gmpolf/gmpolf-2017.10.eb @@ -0,0 +1,32 @@ +easyblock = "Toolchain" + +name = 'gmpolf' +version = '2017.10' + +homepage = '(none)' +description = """gcc and GFortran based compiler toolchain, + MPICH for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '7.2.0-2.29' + +blaslib = 'OpenBLAS' +blasver = '0.2.20' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gmpich' +comp_mpi_tc_version = '2017.08' +comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_version) + +dependencies = [ + ('GCC', gccver), + ('MPICH', '3.2.1', '', ('GCC', gccver)), + (blaslib, blasver, blassuff, ('GCC', gccver)), + ('FFTW', '3.3.7', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..78928684692 --- /dev/null +++ b/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'gmsh' +version = '3.0.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://geuz.org/gmsh' +description = """Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {"usempi": True} + +source_urls = ['http://gmsh.info/src/'] +sources = ['%(name)s-%(version)s-source.tgz'] +checksums = ['9700bcc440d7a6b16a49cbfcdcdc31db33efe60e1f5113774316b6fa4186987b'] + +builddependencies = [ + ('CMake', '3.10.2'), + ('SWIG', '3.0.12', versionsuffix), +] + +dependencies = [ + ('Python', '2.7.14'), + ('PETSc', '3.8.3', '-downloaded-deps'), + ('SLEPc', '3.8.3'), +] + +separate_build_dir = True + +configopts = '-DENABLE_FLTK=0 -DENABLE_WRAP_PYTHON=ON -DENABLE_METIS=1' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/gmsh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/HOME/HOME-0.9-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/h/HOME/HOME-0.9-foss-2017a-Python-2.7.13.eb new file mode 100644 index 00000000000..f98439d6964 --- /dev/null +++ b/easybuild/easyconfigs/h/HOME/HOME-0.9-foss-2017a-Python-2.7.13.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'HOME' +version = '0.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/ListerLab/HOME' +description = """HOME (histogram of methylation) is a python package for differential methylation region (DMR) identification. +The method uses histogram of methylation features and the linear Support Vector Machine (SVM) to identify DMRs +from whole genome bisulfite sequencing (WGBS) data.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = ['https://github.com/ListerLab/HOME/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['HOME-%(version)s_setup.patch'] +checksums = [ + 'bca765e8eb86878f1798e44b313ee8d9670e0dceed7c8be2eec72991ce22041a', # 0.9.tar.gz + 'e9f05b9cd6e3732fb6d478875f8bc821ddc6e21614eb9693a43bf7754ffbb05c', # HOME-0.9_setup.patch +] + +dependencies = [ + ('Python', '2.7.13'), + ('scikit-learn', '0.16.1', versionsuffix), + ('statsmodels', '0.6.1', versionsuffix) +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'HOME'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HOME/HOME-0.9_setup.patch b/easybuild/easyconfigs/h/HOME/HOME-0.9_setup.patch new file mode 100644 index 00000000000..a395bcd7374 --- /dev/null +++ b/easybuild/easyconfigs/h/HOME/HOME-0.9_setup.patch @@ -0,0 +1,20 @@ +Relax library versions to simplify easybuild installations +authir: Ümit Seren (GMI) +diff -ru HOME-0.9/setup.py HOME-0.9.modified/setup.py +--- HOME-0.9/setup.py 2018-04-16 13:10:44.000000000 +0000 ++++ HOME-0.9.modified/setup.py 2018-04-30 08:57:38.578122000 +0000 +@@ -11,10 +11,10 @@ + author = 'akanksha srivastava', + install_requires = [ + 'numpy', +- 'pandas==0.17.1', +- 'scipy==0.16.0', +- 'scikit-learn==0.16.1', +- 'statsmodels==0.6.1', ++ 'pandas', ++ 'scipy', ++ 'scikit-learn', ++ 'statsmodels', + ], + author_email = 'akanksha.srivastava@research.uwa.edu.au', + diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-fosscuda-2018a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-fosscuda-2018a.eb new file mode 100644 index 00000000000..3997af22b36 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-fosscuda-2018a.eb @@ -0,0 +1,22 @@ +name = 'HPL' +version = '2.2' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'fosscuda', 'version': '2018a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] +checksums = [ + 'ac7534163a09e21a5fa763e4e16dfc119bc84043f6e6a807aba666518f8df440', # hpl-2.2.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-giolfc-2017b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-giolfc-2017b.eb new file mode 100644 index 00000000000..b836a7f588d --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-giolfc-2017b.eb @@ -0,0 +1,19 @@ +name = 'HPL' +version = '2.2' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'giolfc', 'version': '2017b'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] +checksums = ['ac7534163a09e21a5fa763e4e16dfc119bc84043f6e6a807aba666518f8df440'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-gmpolf-2017.10.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-gmpolf-2017.10.eb new file mode 100644 index 00000000000..1d4d90ddc21 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-gmpolf-2017.10.eb @@ -0,0 +1,19 @@ +name = 'HPL' +version = '2.2' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'gmpolf', 'version': '2017.10'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] +checksums = ['ac7534163a09e21a5fa763e4e16dfc119bc84043f6e6a807aba666518f8df440'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HiCExplorer/HiCExplorer-2.1.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/h/HiCExplorer/HiCExplorer-2.1.1-foss-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..d3b5bfdc270 --- /dev/null +++ b/easybuild/easyconfigs/h/HiCExplorer/HiCExplorer-2.1.1-foss-2018a-Python-3.6.4.eb @@ -0,0 +1,64 @@ +easyblock = 'Bundle' + +name = 'HiCExplorer' +version = '2.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://hicexplorer.readthedocs.org/' +description = """HiCexplorer addresses the common tasks of Hi-C analysis from processing to visualization.""" + +toolchain = {'name': 'foss', 'version': '2018a'} + +dependencies = [ + ('Python', '3.6.4'), + ('Pysam', '0.14.1', versionsuffix), + ('matplotlib', '2.1.2', versionsuffix), + ('Biopython', '1.71', versionsuffix), + ('PyTables', '3.4.2', versionsuffix), + ('h5py', '2.7.1', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('intervaltree', '2.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/intervaltree'], + 'checksums': ['aca5804b88f70cb49050c37b6de59090570f77a75aec1932966cf69f6a48810b'], + }), + ('pyBigWig', '0.3.11', { + 'modulename': 'pyBigWig', + 'source_urls': ['https://pypi.python.org/packages/source/p/pybigwig'], + 'checksums': ['408ebb40f01c72c77adde4d785a18dabc9abbe9020024e4296b8f6a51a662ae7'], + }), + ('future', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/f/future'], + 'checksums': ['e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb'], + }), + ('cooler', '0.7.6', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cooler'], + 'checksums': ['434559940e933d355dbe14b8188a887eb7e866f0e60ed86e84034521bce81c45'], + }), + ('Jinja2', '2.10', { + 'options': {'modulename': 'jinja2'}, + 'source_urls': ['https://pypi.python.org/packages/source/j/jinja2'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('Unidecode', '1.0.22', { + 'source_urls': ['https://pypi.python.org/packages/source/u/unidecode'], + 'checksums': ['8c33dd588e0c9bc22a76eaa0c715a5434851f726131bd44a6c26471746efabf5'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/deeptools/HiCExplorer/archive/'], + 'checksums': ['7103e20ad93f5afe05ace75023d5fba5f31a7fc8d2e7b52b81555249fcc816e8'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.6-GCCcore-8.1.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.6-GCCcore-8.1.0.eb new file mode 100644 index 00000000000..a6acf99d4a7 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.6-GCCcore-8.1.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.47.6' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '8.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['d91b0295b72a638e4a564f643e4e6d1928779131f628c00f356c13bf336de46f'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.30', '', True), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/ICU/ICU-61.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/i/ICU/ICU-61.1-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..69d4263c64c --- /dev/null +++ b/easybuild/easyconfigs/i/ICU/ICU-61.1-GCCcore-6.4.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'ICU' +version = '61.1' + +homepage = 'http://site.icu-project.org/home' +description = """ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization + support for software applications.""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://download.icu-project.org/files/icu4c/%(version)s'] +sources = ['icu4c-%(version_major)s_%(version_minor)s-src.tgz'] +checksums = ['d007f89ae8a2543a53525c74359b65b36412fa84b3349f1400be6dcf409fafef'] + +builddependencies = [('binutils', '2.28')] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['lib/libicu%s.%s' % (x, SHLIB_EXT) for x in ['data', 'i18n', 'io', 'test', 'tu', 'uc']], + 'dirs': ['bin', 'include/unicode', 'share/icu', 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.7-30-GCCcore-6.4.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.7-30-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..0c50e4a7781 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.7-30-GCCcore-6.4.0.eb @@ -0,0 +1,44 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.0.7-30' + +homepage = 'http://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['https://www.imagemagick.org/download/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['8d3aca87b13dc1c17d28f83326201529e5a2936e9b8ee289377a247c615f272c'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('X11', '20180131'), + ('Ghostscript', '9.23'), + ('JasPer', '2.0.14'), + ('libjpeg-turbo', '1.5.3'), + ('LibTIFF', '4.0.9'), + ('LittleCMS', '2.9'), +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.28'), + ('pkg-config', '0.29.2'), +] + +configopts = "--with-gslib --with-x" + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], +} + +modextravars = {'MAGICK_HOME': '%(installdir)s'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/Imlib2/Imlib2-1.5.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/i/Imlib2/Imlib2-1.5.1-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..8ecf4422874 --- /dev/null +++ b/easybuild/easyconfigs/i/Imlib2/Imlib2-1.5.1-GCCcore-6.4.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'Imlib2' +version = '1.5.1' + +homepage = 'https://docs.enlightenment.org/api/imlib2/html/' +description = """ +This is the Imlib 2 library - a library that does image file loading and +saving as well as rendering, manipulation, arbitrary polygon support, etc. +It does ALL of these operations FAST. Imlib2 also tries to be highly +intelligent about doing them, so writing naive programs can be done +easily, without sacrificing speed. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://sourceforge.net/projects/enlightenment/files/imlib2-src/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b25df9347648cf3dfb784c099139ab24157b1dbd1baa9428f103b683b8a78c61'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('libjpeg-turbo', '1.5.3'), + ('libpng', '1.6.34'), + ('X11', '20180131'), +] + +sanity_check_paths = { + 'files': ['bin/imlib2_%s' % x for x in ['bumpmap', 'colorspace', 'conv', 'grab', 'poly', 'show', 'test', 'view']] + + ['bin/imlib2-config', 'include/Imlib2.h', 'lib/libImlib2.a', 'lib/libImlib2.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2018_update2.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2018_update2.eb new file mode 100644 index 00000000000..df0b0a12292 --- /dev/null +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2018_update2.eb @@ -0,0 +1,17 @@ +name = 'Inspector' +version = '2018_update2' + +homepage = 'http://software.intel.com/en-us/intel-inspector-xe' +description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial + and parallel applications""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['inspector_%(version)s.tar.gz'] +checksums = ['201e29c9b177d21eae619eec090ee1ec703bb7398716377444a4eb685b8bf87b'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/icc/README.md b/easybuild/easyconfigs/i/icc/README.md new file mode 100644 index 00000000000..1ffea21d696 --- /dev/null +++ b/easybuild/easyconfigs/i/icc/README.md @@ -0,0 +1,14 @@ +In order to use these configs you must first download the Intel Parallel Studio XE CPP file. NOT the full bundle! The file should look like this: parallel_studio_xe_2018_update2_composer_edition_for_cpp.tgz + +Next you must specify the license file. There are four options: +* Place it in the following path: ~/licenses/intel/license.lic +* Set an environment variable: `export INTEL_LICENSE_FILE=/path/to/file.lic` +* Set an environment variable: `export LM_LICENSE_FILE=/path/to/file.lic` +* Edit the EB script and modify or add the line `license_file = /path/to/file.lic` + +To install, you must configure EasyBuild to use the right `sourcepath` so it can find the manually downloaded file. There are a number of ways to do this assuming the file is in /home/username/EB_Downloads. +* Pass it as a option on the command line: `eb icc-2018.2.199-GCC-6.4.0-2.28.eb -r --sourcepath=/home/username/EB_Downloads` +* Set an environment variable: `export EASYBUILD_SOURCEPATH=/home/username/EB_Downloads ; eb icc-2018.2.199-GCC-6.4.0-2.28.eb -r` +* Configure a permanent location in ~/.config/easybuild/config.cfg before installing with `eb icc-2018.2.199-GCC-6.4.0-2.28.eb -r` +> [config] +> sourcepath=/home/username/EB_Downloads diff --git a/easybuild/easyconfigs/i/icc/icc-2017.7.259-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2017.7.259-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..675cf2ba85e --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2017.7.259-GCC-6.4.0-2.28.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild + +name = 'icc' +version = '2017.7.259' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "Intel C and C++ compilers" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] + +checksums = ['3065e3ea0e489fe6d50aea725ac095422c13aa51b88d02f6380af06b708dbb98'] + +gccver = '6.4.0' +binutilsver = '2.28' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/README.md b/easybuild/easyconfigs/i/ifort/README.md new file mode 100644 index 00000000000..d1e78523730 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/README.md @@ -0,0 +1,14 @@ +In order to use these configs you must first download the Intel Parallel Studio XE Fortran file. NOT the full bundle! The file should look like this: parallel_studio_xe_2018_update2_composer_edition_for_fortran.tgz + +Next you must specify the license file. There are four options: +* Place it in the following path: ~/licenses/intel/license.lic +* Set an environment variable: `export INTEL_LICENSE_FILE=/path/to/file.lic` +* Set an environment variable: `export LM_LICENSE_FILE=/path/to/file.lic` +* Edit the EB script and modify or add the line `license_file = /path/to/file.lic` + +To install, you must configure EasyBuild to use the right `sourcepath` so it can find the manually downloaded file. There are a number of ways to do this assuming the file is in /home/username/EB_Downloads. +* Pass it as a option on the command line: `eb ifort-2018.2.199-GCC-6.4.0-2.28.eb -r --sourcepath=/home/username/EB_Downloads` +* Set an environment variable: `export EASYBUILD_SOURCEPATH=/home/username/EB_Downloads ; eb ifort-2018.2.199-GCC-6.4.0-2.28.eb -r` +* Configure a permanent location in ~/.config/easybuild/config.cfg before installing with `eb ifort-2018.2.199-GCC-6.4.0-2.28.eb -r` +> [config] +> sourcepath=/home/username/EB_Downloads diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.7.259-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.7.259-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..8fd3c0675b7 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.7.259-GCC-6.4.0-2.28.eb @@ -0,0 +1,40 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild + +name = 'ifort' +version = '2017.7.259' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "Intel Fortran compiler" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] + +checksums = [ + # parallel_studio_xe_2017_update7_composer_edition_for_fortran.tgz + 'b33908eacecdac12ddf30819349434c3982f4a2aea5614fe44e8cc879ced81e2', + '7241e492a5f7ba4e62e8106c97f585c2fd931e32886d886f7bf0a9020e421325', # ifort_2017_no_mpi_mic_dependency.patch +] + +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2017_no_mpi_mic_dependency.patch'] + +gccver = '6.4.0' +binutilsver = '2.28' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_', 'intel-gdb(?!.*mic)'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb index 229575d9aa9..acc63120383 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb @@ -16,6 +16,8 @@ checksums = ['f72546df27f5ebb0941b5d21fd804e34'] dontcreateinstalldir = 'True' +components = ['intel-mkl'] + license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb index 5cf1169219f..51e8a3461a9 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb @@ -16,6 +16,8 @@ checksums = ['f72546df27f5ebb0941b5d21fd804e34'] dontcreateinstalldir = 'True' +components = ['intel-mkl'] + license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb index 59e82c59103..d98d8f0fd38 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb @@ -16,6 +16,8 @@ checksums = ['f72546df27f5ebb0941b5d21fd804e34'] dontcreateinstalldir = 'True' +components = ['intel-mkl'] + license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb index c5041e44d7e..ebe3bf0517a 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb @@ -16,6 +16,8 @@ checksums = ['f72546df27f5ebb0941b5d21fd804e34'] dontcreateinstalldir = 'True' +components = ['intel-mkl'] + license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb index 5fdaf87f4ca..b9d95449e02 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb @@ -16,6 +16,8 @@ checksums = ['3cdcb739ab5ab1e047eb130b9ffdd8d0'] dontcreateinstalldir = 'True' +components = ['intel-mkl'] + license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-gimpi-2017a.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-gimpi-2017a.eb index aaa3568ab05..a003630b703 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-gimpi-2017a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-gimpi-2017a.eb @@ -14,6 +14,8 @@ checksums = ['7911c0f777c4cb04225bf4518088939e'] dontcreateinstalldir = 'True' +components = ['intel-mkl'] + license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb index 8f2a455c2d3..890e13c11b6 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb @@ -16,6 +16,8 @@ checksums = ['7911c0f777c4cb04225bf4518088939e'] dontcreateinstalldir = 'True' +components = ['intel-mkl'] + license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb index 1b5c22920c7..8b4fb3f6312 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb @@ -16,6 +16,8 @@ checksums = ['7911c0f777c4cb04225bf4518088939e'] dontcreateinstalldir = 'True' +components = ['intel-mkl'] + license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb index 470e9458e02..d518da619e8 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb @@ -16,6 +16,8 @@ checksums = ['7911c0f777c4cb04225bf4518088939e'] dontcreateinstalldir = 'True' +components = ['intel-mkl'] + license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb index a6925bd1bb2..2b75677f007 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb @@ -16,6 +16,8 @@ checksums = ['7911c0f777c4cb04225bf4518088939e'] dontcreateinstalldir = 'True' +components = ['intel-mkl'] + license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb index 96112a19235..35e5b716e18 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb @@ -16,6 +16,8 @@ checksums = ['ef39a12dcbffe5f4a0ef141b8759208c'] dontcreateinstalldir = 'True' +components = ['intel-mkl'] + interfaces = True postinstallcmds = [ diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-gompi-2017b.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-gompi-2017b.eb index 2591539c25b..941c7c55065 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-gompi-2017b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-gompi-2017b.eb @@ -16,6 +16,8 @@ checksums = ['fd7295870fa164d6138c9818304f25f2bb263c814a6c6539c9fe4e104055f1ca'] dontcreateinstalldir = 'True' +components = ['intel-mkl'] + license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb index 9199c8b2b8f..f75eb9307d3 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb @@ -14,6 +14,8 @@ checksums = ['fd7295870fa164d6138c9818304f25f2bb263c814a6c6539c9fe4e104055f1ca'] dontcreateinstalldir = 'True' +components = ['intel-mkl'] + interfaces = True postinstallcmds = [ diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iompi-2017b.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iompi-2017b.eb index 74a22643af0..00757dc56fe 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iompi-2017b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iompi-2017b.eb @@ -16,6 +16,8 @@ checksums = ['fd7295870fa164d6138c9818304f25f2bb263c814a6c6539c9fe4e104055f1ca'] dontcreateinstalldir = 'True' +components = ['intel-mkl'] + license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.4.239-iimpi-2017.09.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.4.239-iimpi-2017.09.eb index 17d55948d6d..0d77a694cf8 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.4.239-iimpi-2017.09.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.4.239-iimpi-2017.09.eb @@ -14,6 +14,8 @@ checksums = ['dcac591ed1e95bd72357fd778edba215a7eab9c6993236373231cc16c200c92a'] dontcreateinstalldir = 'True' +components = ['intel-mkl'] + interfaces = True postinstallcmds = [ diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.0.128-iimpi-2018.00.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.0.128-iimpi-2018.00.eb index 938f4a92b3e..118a71a3310 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.0.128-iimpi-2018.00.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.0.128-iimpi-2018.00.eb @@ -16,6 +16,8 @@ checksums = ['c368baa40ca88057292512534d7fad59fa24aef06da038ea0248e7cd1e280cec'] dontcreateinstalldir = 'True' +components = ['intel-mkl'] + license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018.01.eb index 7d288d9211e..9e5eacd4164 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018.01.eb @@ -16,6 +16,8 @@ checksums = ['f6dc263fc6f3c350979740a13de1b1e8745d9ba0d0f067ece503483b9189c2ca'] dontcreateinstalldir = 'True' +components = ['intel-mkl'] + license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb index c91459f4fc8..c5a605c4b63 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb @@ -16,6 +16,8 @@ checksums = ['f6dc263fc6f3c350979740a13de1b1e8745d9ba0d0f067ece503483b9189c2ca'] dontcreateinstalldir = 'True' +components = ['intel-mkl'] + license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iompi-2018a.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iompi-2018a.eb index 489ce83e772..16c929d513a 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iompi-2018a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iompi-2018a.eb @@ -16,6 +16,8 @@ checksums = ['f6dc263fc6f3c350979740a13de1b1e8745d9ba0d0f067ece503483b9189c2ca'] dontcreateinstalldir = 'True' +components = ['intel-mkl'] + license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iimpi-2018.02.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iimpi-2018.02.eb index 59666c45f13..3a413da4629 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iimpi-2018.02.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iimpi-2018.02.eb @@ -16,6 +16,8 @@ checksums = ['e28d12173bef9e615b0ded2f95f59a42b3e9ad0afa713a79f8801da2bfb31936'] dontcreateinstalldir = 'True' +components = ['intel-mkl'] + license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iompi-2018.02.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iompi-2018.02.eb index 9ec7bade843..cd34e04f641 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iompi-2018.02.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iompi-2018.02.eb @@ -16,6 +16,8 @@ checksums = ['e28d12173bef9e615b0ded2f95f59a42b3e9ad0afa713a79f8801da2bfb31936'] dontcreateinstalldir = 'True' +components = ['intel-mkl'] + license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/impi/impi-2017.3.196-gcccuda-2017b.eb b/easybuild/easyconfigs/i/impi/impi-2017.3.196-gcccuda-2017b.eb new file mode 100644 index 00000000000..3db0955ff75 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2017.3.196-gcccuda-2017b.eb @@ -0,0 +1,35 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild + +name = 'impi' +version = '2017.3.196' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'gcccuda', 'version': '2017b'} + +sources = ['l_mpi_%(version)s.tgz'] + +checksums = ['dad9efbc5bbd3fd27cce7e1e2507ad77f342d5ecc929747ae141c890e7fb87f0'] + +dontcreateinstalldir = 'True' + +components = ['intel-mpi', 'intel-psxe', 'intel-imb'] + +license_file = HOME + '/licenses/intel/license.lic' + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +postinstallcmds = [ + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', + 'ln -s %(installdir)s/lib64/libmpigc4.so %(installdir)s/lib64/libmpichcxx.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so', +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_172.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_172.eb new file mode 100644 index 00000000000..55753333859 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_172.eb @@ -0,0 +1,17 @@ +name = 'Java' +version = '1.8.0_172' + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from +# http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] +checksums = ['28a00b9400b6913563553e09e8024c286b506d8523334c93ddec6c9ec7e9d346'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/README.md b/easybuild/easyconfigs/j/Java/README.md new file mode 100644 index 00000000000..10935b6be69 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/README.md @@ -0,0 +1,8 @@ +In order to use these configs you must first download Java from [Oracle](http://www.oracle.com/technetwork/java/javase/downloads/index.html). The file name should look like this: jdk-8u162-linux-x64.tar.gz + +To install, you must configure EasyBuild to use the right `sourcepath` so it can find the manually downloaded file. There are a number of ways to do this assuming the file is in /home/username/EB_Downloads. +* Pass it as a option on the command line: `eb Java-1.8.0_162.eb -r --sourcepath=/home/username/EB_Downloads` +* Set an environment variable:`export EASYBUILD_SOURCEPATH=/home/username/EB_Downloads ; eb Java-1.8.0_162.eb -r` +* Configure a permanent location in ~/.config/easybuild/config.cfg before installing with `eb Java-1.8.0_162.eb -r` +> [config] +> sourcepath=/home/username/EB_Downloads diff --git a/easybuild/easyconfigs/k/KmerGenie/KmerGenie-1.7044-intel-2017a.eb b/easybuild/easyconfigs/k/KmerGenie/KmerGenie-1.7044-intel-2017a.eb new file mode 100644 index 00000000000..d2ed5e5716f --- /dev/null +++ b/easybuild/easyconfigs/k/KmerGenie/KmerGenie-1.7044-intel-2017a.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'KmerGenie' +version = '1.7044' + +homepage = 'http://kmergenie.bx.psu.edu/' +description = 'KmerGenie estimates the best k-mer length for genome de novo assembly.' + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://kmergenie.bx.psu.edu'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['46f2a08a2d7b1885414143e436829dd7e61fcc31ec4e429433e516a168d2978e'] + +dependencies = [ + ('Python', '2.7.13'), + ('R', '3.4.0', '-X11-20170314'), + ('zlib', '1.2.11'), +] + +files_to_copy = ['*'] + +sanity_check_paths = { + 'files': ['kmergenie', 'specialk'], + 'dirs': ['minia', 'ntCard'] +} + +modextrapaths = {'PATH': ['']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-foss-2018a.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-foss-2018a.eb new file mode 100644 index 00000000000..69fd8eab7da --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-foss-2018a.eb @@ -0,0 +1,35 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exequiel Sepulveda +# License:: MIT/GPL +# +# Notes:: Adopted from EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Fotis Georgatos +## + +easyblock = 'ConfigureMake' + +name = 'LZO' +version = '2.10' + +homepage = 'http://www.oberhumer.com/opensource/lzo/' +description = "Portable lossless data compression library" + +toolchain = {'name': 'foss', 'version': '2018a'} +toolchainopts = {'pic': True} + +source_urls = [homepage + 'download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072'] + +runtest = 'test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib', 'include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.4.2-intel-2018a.eb b/easybuild/easyconfigs/l/Libint/Libint-2.4.2-intel-2018a.eb index d37b23b5c69..f36862909d7 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.4.2-intel-2018a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.4.2-intel-2018a.eb @@ -6,7 +6,7 @@ description = """Libint library is used to evaluate the traditional (electron re matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" toolchain = {'name': 'intel', 'version': '2018a'} -toolchainopts = {'pic': True} +toolchainopts = {'pic': True, 'cstd': 'c++11'} source_urls = ['https://github.com/evaleev/libint/archive'] sources = ['v%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.9-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.9-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..9290287df56 --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.9-GCCcore-6.4.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.9' + +homepage = 'http://www.littlecms.com/' +description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, + with special focus on accuracy and performance. """ + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://sourceforge.net/projects/lcms/files/lcms/%(version)s/'] +sources = ['lcms2-%(version)s.tar.gz'] +checksums = ['48c6fdf98396fa245ed86e622028caf49b96fa22f3e5734f853f806fbc8e7d20'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.28'), +] + +dependencies = [('libjpeg-turbo', '1.5.3')] + +sanity_check_paths = { + 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h', + 'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], + 'dirs': ['share/man'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.19.1-foss-2017b.eb b/easybuild/easyconfigs/l/libdap/libdap-3.19.1-foss-2017b.eb new file mode 100644 index 00000000000..d8abaf42875 --- /dev/null +++ b/easybuild/easyconfigs/l/libdap/libdap-3.19.1-foss-2017b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libdap' +version = '3.19.1' + +homepage = 'http://opendap.org/download/libdap' +description = """A C++ SDK which contains an implementation of DAP 2.0 + and the development versions of DAP3, up to 3.4. + This includes both Client- and Server-side support classes.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['http://www.opendap.org/pub/source/'] +sources = [SOURCE_TAR_GZ] +checksums = ['5215434bacf385ba3f7445494ce400a5ade3995533d8d38bb97fcef1478ad33e'] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('cURL', '7.56.0'), + ('libxml2', '2.9.4'), + ('LibUUID', '1.0.3'), +] + +sanity_check_paths = { + 'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/libdap.a', 'lib/libdap.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.19.1-intel-2017b.eb b/easybuild/easyconfigs/l/libdap/libdap-3.19.1-intel-2017b.eb index 3da2d768b73..117b975846b 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.19.1-intel-2017b.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.19.1-intel-2017b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} source_urls = ['http://www.opendap.org/pub/source/'] sources = [SOURCE_TAR_GZ] -checksums = ['fb7014b6047cf3fa47d05c0faf258636f664c5fc232ff0886a78dfc5aae29f8f'] +checksums = ['5215434bacf385ba3f7445494ce400a5ade3995533d8d38bb97fcef1478ad33e'] builddependencies = [ ('Bison', '3.0.4'), diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-GCCcore-5.4.0.eb index b1d941c8c59..b3a14a80924 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-GCCcore-5.4.0.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} builddependencies = [ ('binutils', '2.26'), + ('pkg-config', '0.29.1'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb index 5d9e8ac9385..4df8720b54e 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb @@ -8,9 +8,13 @@ description = """Direct Rendering Manager runtime library.""" source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['73615b9c1c4852e5ce045efa19c866e8df98e396b2443bf859eea05574ecb64f'] toolchain = {'name': 'foss', 'version': '2016b'} +builddependencies = [ + ('pkg-config', '0.29.1'), +] dependencies = [ ('X11', '20160819'), ] diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb index 9fb07a29545..8ba942cd24e 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb @@ -8,9 +8,13 @@ description = """Direct Rendering Manager runtime library.""" source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['73615b9c1c4852e5ce045efa19c866e8df98e396b2443bf859eea05574ecb64f'] toolchain = {'name': 'intel', 'version': '2016b'} +builddependencies = [ + ('pkg-config', '0.29.1'), +] dependencies = [ ('X11', '20160819'), ] diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-GCCcore-6.3.0.eb index d6e3c7e9a15..71405b06c2a 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-GCCcore-6.3.0.eb @@ -10,17 +10,15 @@ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] -checksums = [ - '6e3fb50d7500acf06f7eed44d5b1d33cda26aef7f5ae6667ddcc626b435c2531', # libdrm-2.4.76.tar.gz -] +checksums = ['6e3fb50d7500acf06f7eed44d5b1d33cda26aef7f5ae6667ddcc626b435c2531'] +builddependencies = [ + ('binutils', '2.27'), + ('pkg-config', '0.29.2'), +] dependencies = [ ('X11', '20170314'), ] -builddependencies = [ - # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', True), -] sanity_check_paths = { 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb index a8a5a109c80..6fc624e27e3 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb @@ -8,9 +8,13 @@ description = """Direct Rendering Manager runtime library.""" source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['6e3fb50d7500acf06f7eed44d5b1d33cda26aef7f5ae6667ddcc626b435c2531'] toolchain = {'name': 'intel', 'version': '2017a'} +builddependencies = [ + ('pkg-config', '0.29.1'), +] dependencies = [ ('X11', '20170314'), ] diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.88-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.88-GCCcore-6.4.0.eb index b42941af78c..ced77432f6a 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.88-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.88-GCCcore-6.4.0.eb @@ -12,7 +12,10 @@ source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['a8b458db6a73c717baee2e249d39511fb6f5c0f5f24dee2770935eddeda1a017'] -builddependencies = [('binutils', '2.28')] +builddependencies = [ + ('binutils', '2.28'), + ('pkg-config', '0.29.2'), +] dependencies = [('X11', '20171023')] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.91-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.91-GCCcore-6.4.0.eb index 4b52f0da878..fa9a8cceb52 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.91-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.91-GCCcore-6.4.0.eb @@ -12,7 +12,10 @@ source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['c8ea3343d5bfc356550f0b5632403359d050fa09cf05d61e96e73adba0c407a9'] -builddependencies = [('binutils', '2.28')] +builddependencies = [ + ('binutils', '2.28'), + ('pkg-config', '0.29.2'), +] dependencies = [('X11', '20180131')] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.4.2-foss-2018a.eb b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.4.2-foss-2018a.eb new file mode 100644 index 00000000000..f1d5c352567 --- /dev/null +++ b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.4.2-foss-2018a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libgeotiff' +version = '1.4.2' + +homepage = 'https://directory.fsf.org/wiki/Libgeotiff' +description = "Library for reading and writing coordinate system information from/to GeoTIFF files" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = [ + 'http://download.osgeo.org/geotiff/libgeotiff/', + 'ftp://ftp.remotesensing.org/pub/libgeotiff/', +] + +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['ad87048adb91167b07f34974a8e53e4ec356494c29f1748de95252e8f81a5e6e'] + +dependencies = [ + ('zlib', '1.2.11'), + ('LibTIFF', '4.0.9'), + ('PROJ', '5.0.0'), + ('libjpeg-turbo', '1.5.3'), +] + +configopts = ' --with-libtiff=$EBROOTLIBTIFF --with-proj=$EBROOTPROJ --with-zlib=$EBROOTZLIB' +configopts += ' --with-jpeg=$EBROOTLIBJPEGMINTURBO' + +sanity_check_paths = { + 'files': ['bin/listgeo', 'lib/libgeotiff.a', 'lib/libgeotiff.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.16-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.16-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..d1bbd0e7c97 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.16-GCCcore-6.4.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.16' + +homepage = 'http://doc.libsodium.org/' + +description = """ + Sodium is a modern, easy-to-use software library for encryption, decryption, + signatures, password hashing and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.libsodium.org/libsodium/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['eeadc7e1e1bcef09680fb4837d448fbdf57224978f865ac1c16745868fbd0533'] + +builddependencies = [ + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.1-gimkl-2017a.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-gimkl-2017a.eb new file mode 100644 index 00000000000..bb19d10aec5 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-gimkl-2017a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '3.0.1' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] +checksums = ['836692f2ab60ec3aca0cca105ed5d0baa7d182be07cc9d0daa7b80ee1362caf7'] + +configopts = '--enable-static --enable-shared --enable-fortran' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.3.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/likwid/likwid-4.3.2-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..8d01751322a --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-4.3.2-GCCcore-6.4.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '4.3.2' + +homepage = 'http://code.google.com/p/likwid/' + +description = """ + Likwid stands for Like I knew what I am doing. This project contributes easy + to use command line tools for Linux to support programmers in developing high + performance multi threaded programs. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +# https://github.com/RRZE-HPC/likwid/archive/4.2.0.tar.gz +source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['fd39529854b8952e7530da1684835aa43ac6ce2169f5ebd1fb2a481f6fb288ac'] + +builddependencies = [ + ('binutils', '2.28'), +] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg' + +maxparallel = 1 + +installopts = 'PREFIX=%(installdir)s INSTALL_CHOWN="" BUILDFREQ=""' + +sanity_check_paths = { + 'files': ["bin/likwid-memsweeper", "bin/likwid-mpirun", "bin/likwid-perfctr", + "bin/likwid-perfscope", "bin/likwid-pin", "bin/likwid-powermeter", + "bin/likwid-topology", "lib/liblikwidpin.%s" % SHLIB_EXT, + "lib/liblikwid.%s" % SHLIB_EXT], + 'dirs': ["man/man1"] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/lxml/lxml-4.2.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/l/lxml/lxml-4.2.0-intel-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..e133510b022 --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-4.2.0-intel-2018a-Python-3.6.4.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'lxml' +version = '4.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['http://lxml.de/files/'] +sources = [SOURCE_TGZ] +checksums = ['7d96fbb5f23a62300aa9bef7d286cd61aca8902357619c8708c0290aba5df73f'] + +dependencies = [ + ('Python', '3.6.4'), + ('libxml2', '2.9.7'), + ('libxslt', '1.1.32'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb new file mode 100644 index 00000000000..3952846bcd7 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.18' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '8.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.30', '', True)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.397-intel-2018a-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.397-intel-2018a-with-extensions.eb new file mode 100644 index 00000000000..e0f106a6239 --- /dev/null +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.397-intel-2018a-with-extensions.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 7.305 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'MAFFT' +version = '7.397' +versionsuffix = '-with-extensions' + +homepage = 'https://mafft.cbrc.jp/alignment/software/' +description = """MAFFT is a multiple sequence alignment program + for unix-like operating systems. It offers a range of multiple + alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), + FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = [homepage] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s-src.tgz'] +checksums = ['05938ecea648e8dec0bc163692cdb5bffa8ffea928ca85d42d7e55b8516a3cb3'] + +skipsteps = ['configure'] +start_dir = 'core' +installopts = 'PREFIX=%(installdir)s' + +modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} + +sanity_check_paths = { + 'files': ['bin/mafft'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MCL/MCL-14.137-GCCcore-6.4.0-Perl-5.26.1.eb b/easybuild/easyconfigs/m/MCL/MCL-14.137-GCCcore-6.4.0-Perl-5.26.1.eb new file mode 100644 index 00000000000..a7cac877f13 --- /dev/null +++ b/easybuild/easyconfigs/m/MCL/MCL-14.137-GCCcore-6.4.0-Perl-5.26.1.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'MCL' +version = '14.137' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://micans.org/mcl/' +description = """The MCL algorithm is short for the Markov Cluster Algorithm, a fast +and scalable unsupervised cluster algorithm for graphs (also known as networks) based +on simulation of (stochastic) flow in graphs. """ + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://micans.org/%(namelower)s/src/'] +sources = ['%(namelower)s-%(version_major)s-%(version_minor)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_fixperl.patch', +] +checksums = [ + 'b5786897a8a8ca119eb355a5630806a4da72ea84243dba85b19a86f14757b497', # mcl-14-137.tar.gz + '46988a287b2ee400a54fa485176d043b2a2d6589b6257cc6cf9c21689ea3842d', # MCL-14.137_fixperl.patch +] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('Perl', '5.26.1'), +] + +configopts = '--enable-blast ' + +sanity_check_paths = { + 'files': ['bin/mcl', 'bin/mcxdeblast'], + 'dirs': ['share'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MCL/MCL-14.137-foss-2016a.eb b/easybuild/easyconfigs/m/MCL/MCL-14.137-foss-2016a.eb index cade8a0bf76..3b1d5e2c393 100644 --- a/easybuild/easyconfigs/m/MCL/MCL-14.137-foss-2016a.eb +++ b/easybuild/easyconfigs/m/MCL/MCL-14.137-foss-2016a.eb @@ -12,6 +12,13 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://micans.org/%(namelower)s/src/'] sources = ['%(namelower)s-%(version_major)s-%(version_minor)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_fixperl.patch', +] +checksums = [ + 'b5786897a8a8ca119eb355a5630806a4da72ea84243dba85b19a86f14757b497', # mcl-14-137.tar.gz + '46988a287b2ee400a54fa485176d043b2a2d6589b6257cc6cf9c21689ea3842d', # MCL-14.137_fixperl.patch +] sanity_check_paths = { 'files': ['bin/mcl'], diff --git a/easybuild/easyconfigs/m/MCL/MCL-14.137-intel-2016b.eb b/easybuild/easyconfigs/m/MCL/MCL-14.137-intel-2016b.eb index 11b922bce75..e319434ae92 100644 --- a/easybuild/easyconfigs/m/MCL/MCL-14.137-intel-2016b.eb +++ b/easybuild/easyconfigs/m/MCL/MCL-14.137-intel-2016b.eb @@ -12,6 +12,13 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['http://micans.org/%(namelower)s/src/'] sources = ['%(namelower)s-%(version_major)s-%(version_minor)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_fixperl.patch', +] +checksums = [ + 'b5786897a8a8ca119eb355a5630806a4da72ea84243dba85b19a86f14757b497', # mcl-14-137.tar.gz + '46988a287b2ee400a54fa485176d043b2a2d6589b6257cc6cf9c21689ea3842d', # MCL-14.137_fixperl.patch +] sanity_check_paths = { 'files': ['bin/mcl'], diff --git a/easybuild/easyconfigs/m/MCL/MCL-14.137_fixperl.patch b/easybuild/easyconfigs/m/MCL/MCL-14.137_fixperl.patch new file mode 100644 index 00000000000..25cf55e4055 --- /dev/null +++ b/easybuild/easyconfigs/m/MCL/MCL-14.137_fixperl.patch @@ -0,0 +1,140 @@ +# fix /usr/loca/bin/perl +# May 03rd 2018 by B. Hajgato (Free University Brussels - VUB) +diff -ru mcl-14-137.orig/doc/minimcl mcl-14-137/doc/minimcl +--- mcl-14-137.orig/doc/minimcl 2006-02-27 00:18:05.000000000 +0100 ++++ mcl-14-137/doc/minimcl 2018-05-03 10:43:10.577298454 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl -w ++#!/usr/bin/env perl -w + + # (C) Copyright 2006 Stijn van Dongen + # +diff -ru mcl-14-137.orig/graphs/make-falkner.pl mcl-14-137/graphs/make-falkner.pl +--- mcl-14-137.orig/graphs/make-falkner.pl 2007-07-17 11:20:33.000000000 +0200 ++++ mcl-14-137/graphs/make-falkner.pl 2018-05-03 10:41:32.023704666 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl -w + + use Getopt::Long; + use strict; +diff -ru mcl-14-137.orig/scripts/clmsnare mcl-14-137/scripts/clmsnare +--- mcl-14-137.orig/scripts/clmsnare 2007-07-02 12:16:01.000000000 +0200 ++++ mcl-14-137/scripts/clmsnare 2018-05-03 10:42:09.148798258 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl -w + + # (C) Copyright 2007 Stijn van Dongen + # +diff -ru mcl-14-137.orig/scripts/clxdo mcl-14-137/scripts/clxdo +--- mcl-14-137.orig/scripts/clxdo 2014-04-25 12:04:38.000000000 +0200 ++++ mcl-14-137/scripts/clxdo 2018-05-03 10:46:25.142547838 +0200 +@@ -83,7 +83,7 @@ + require_num 1 "+" + mx=$2 + mcxdump -imx $mx --no-values --dump-lines -o - \ +-| /usr/local/bin/perl -ane '$ct{@F-1}++; END { print map { "$_ $ct{$_}\n" } sort { $a <=> $b } keys %ct; }' ++| /usr/bin/env perl -ane '$ct{@F-1}++; END { print map { "$_ $ct{$_}\n" } sort { $a <=> $b } keys %ct; }' + ;; + + +@@ -116,7 +116,7 @@ + shift 2 + for mx in $@; do + mcxdump -imx $mx --no-values --dump-lines -o - \ +- | /usr/local/bin/perl -ane '$ct{@F-1}++; END {%i = map { ($_, 1) } grep { $_ >= $ENV{CLXDO_VAL1}; } keys %ct; ($lt, $n_lt, $gq, $n_gq) = (0,0,0,0); for my $x (keys %ct) { if ($i{$x}) { $n_gq += $ct{$x}; $gq += $x * $ct{$x}; } else { $n_lt += $ct{$x}; $lt += $x * $ct{$x} } } print "$n_lt $lt $n_gq $gq\n"; }' ++ | /usr/bin/env perl -ane '$ct{@F-1}++; END {%i = map { ($_, 1) } grep { $_ >= $ENV{CLXDO_VAL1}; } keys %ct; ($lt, $n_lt, $gq, $n_gq) = (0,0,0,0); for my $x (keys %ct) { if ($i{$x}) { $n_gq += $ct{$x}; $gq += $x * $ct{$x}; } else { $n_lt += $ct{$x}; $lt += $x * $ct{$x} } } print "$n_lt $lt $n_gq $gq\n"; }' + done + ;; + +diff -ru mcl-14-137.orig/scripts/docme mcl-14-137/scripts/docme +--- mcl-14-137.orig/scripts/docme 2013-05-16 12:32:13.000000000 +0200 ++++ mcl-14-137/scripts/docme 2018-05-03 10:43:04.448448095 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl -w ++#!/usr/bin/env perl -w + + # This program matches + # A) +diff -ru mcl-14-137.orig/scripts/gengraph mcl-14-137/scripts/gengraph +--- mcl-14-137.orig/scripts/gengraph 2009-09-24 11:36:29.000000000 +0200 ++++ mcl-14-137/scripts/gengraph 2018-05-03 10:42:52.678735459 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl -w ++#!/usr/bin/env perl -w + + # (C) Copyright 2009 Stijn van Dongen + # +diff -ru mcl-14-137.orig/scripts/minimcl mcl-14-137/scripts/minimcl +--- mcl-14-137.orig/scripts/minimcl 2009-06-09 12:51:04.000000000 +0200 ++++ mcl-14-137/scripts/minimcl 2018-05-03 10:42:42.452985126 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl -w ++#!/usr/bin/env perl -w + + # (C) Copyright 2006, 2007, 2008, 2009 Stijn van Dongen + # +diff -ru mcl-14-137.orig/scripts/mlm-fifofum mcl-14-137/scripts/mlm-fifofum +--- mcl-14-137.orig/scripts/mlm-fifofum 2008-03-12 23:50:37.000000000 +0100 ++++ mcl-14-137/scripts/mlm-fifofum 2018-05-03 10:41:50.300258445 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl -w ++#!/usr/bin/env perl -w + + # (C) Copyright 2007 Stijn van Dongen + # +diff -ru mcl-14-137.orig/scripts/mlm-quilt mcl-14-137/scripts/mlm-quilt +--- mcl-14-137.orig/scripts/mlm-quilt 2009-05-20 00:30:25.000000000 +0200 ++++ mcl-14-137/scripts/mlm-quilt 2018-05-03 10:42:58.911583281 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl -w ++#!/usr/bin/env perl -w + + # (C) Copyright 2007 Stijn van Dongen + # +diff -ru mcl-14-137.orig/scripts/mlm-summary mcl-14-137/scripts/mlm-summary +--- mcl-14-137.orig/scripts/mlm-summary 2007-11-06 17:05:30.000000000 +0100 ++++ mcl-14-137/scripts/mlm-summary 2018-05-03 10:41:43.416426514 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl -w ++#!/usr/bin/env perl -w + + # (C) Copyright 2007 Stijn van Dongen + # +diff -ru mcl-14-137.orig/scripts/movgraph mcl-14-137/scripts/movgraph +--- mcl-14-137.orig/scripts/movgraph 2009-09-24 11:52:43.000000000 +0200 ++++ mcl-14-137/scripts/movgraph 2018-05-03 10:42:00.405011738 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl -w ++#!/usr/bin/env perl -w + + # (C) Copyright 2009 Stijn van Dongen + # +diff -ru mcl-14-137.orig/scripts/tree3.pl mcl-14-137/scripts/tree3.pl +--- mcl-14-137.orig/scripts/tree3.pl 2010-06-08 23:03:05.000000000 +0200 ++++ mcl-14-137/scripts/tree3.pl 2018-05-03 10:42:34.168187403 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl -w ++#!/usr/bin/env perl -w + + use strict; + use Data::Dumper; +diff -ru mcl-14-137.orig/src/alien/oxygen/src/mcxdeblast mcl-14-137/src/alien/oxygen/src/mcxdeblast +--- mcl-14-137.orig/src/alien/oxygen/src/mcxdeblast 2009-03-24 17:09:46.000000000 +0100 ++++ mcl-14-137/src/alien/oxygen/src/mcxdeblast 2018-05-03 10:41:22.716931889 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl -w ++#!/usr/bin/env perl -w + + use Getopt::Long; + +diff -ru mcl-14-137.orig/testing/stream/abc-pairs.pl mcl-14-137/testing/stream/abc-pairs.pl +--- mcl-14-137.orig/testing/stream/abc-pairs.pl 2008-10-28 23:37:10.000000000 +0100 ++++ mcl-14-137/testing/stream/abc-pairs.pl 2018-05-03 10:40:42.597911375 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/env perl + + use strict; + use Getopt::Long; diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.0.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/MPFR/MPFR-4.0.1-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..16dd2310e27 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.0.1-GCCcore-6.4.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '4.0.1' + +homepage = 'http://www.mpfr.org' + +description = """ + The MPFR library is a C library for multiple-precision floating-point + computations with correct rounding. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['a4d97610ba8579d380b384b225187c250ef88cfe1d5e7226b89519374209b86b'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('GMP', '6.1.2'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/Maple/Maple-2017.2.eb b/easybuild/easyconfigs/m/Maple/Maple-2017.2.eb new file mode 100644 index 00000000000..1c83d4243cd --- /dev/null +++ b/easybuild/easyconfigs/m/Maple/Maple-2017.2.eb @@ -0,0 +1,21 @@ +name = 'Maple' +version = '2017.2' + +homepage = 'http://www.maplesoft.com/products/maple/' +description = """Maple combines the world's most powerful mathematical computation engine with an intuitive, + 'clickable' user interface.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [ + '%(name)s%(version_major)s.0LinuxX64Installer.run', + '%(name)s%(version)sLinuxX64Upgrade.run', +] +checksums = [ + 'ed36e721b889f3b6ce5856542e8754690c874f5708f3857714f420176a3c5407', # Maple2017.0LinuxX64Installer.run + '1e874c7f8ec9013dfd55f02aafc66f137089949c85eae6f5b78c340282ac1548', # Maple2017.2LinuxX64Upgrade.run +] + +license_server = 'license.example.com' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-11.3.0.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-11.3.0.eb new file mode 100644 index 00000000000..d3cf561129c --- /dev/null +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-11.3.0.eb @@ -0,0 +1,17 @@ +name = 'Mathematica' +version = '11.3.0' + +homepage = 'http://www.wolfram.com/mathematica' +description = """Mathematica is a computational software program used in many scientific, engineering, mathematical +and computing fields.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['Mathematica_%(version)s_LINUX.sh'] +checksums = ['0fcfe208c1eac8448e7be3af0bdb84370b17bd9c5d066c013928c8ee95aed10e'] + +license_server = 'license.example.com' + +sanity_check_commands = [('mathematica', '--version')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.10-foss-2018a.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.10-foss-2018a.eb new file mode 100755 index 00000000000..f82d58eb94a --- /dev/null +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.10-foss-2018a.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# The Francis Crick Institute +# adam.huffman@crick.ac.uk + +easyblock = 'MakeCp' + +name = 'minimap2' +version = '2.10' + +homepage = 'https://github.com/lh3/minimap2' +description = """Minimap2 is a fast sequence mapping and alignment program that can find overlaps between + long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed + alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to + ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited + test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace + BWA-MEM for long reads and contig alignment.""" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar.bz2'] +checksums = ['52b36f726ec00bfca4a2ffc23036d1a2b5f96f0aae5a92fd826be6680c481c20'] + +files_to_copy = [(['%(name)s'], 'bin'), 'LICENSE.txt', 'NEWS.md', 'README.md', (['%(name)s.1'], 'share/man/man1')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.7.4-foss-2017b.eb b/easybuild/easyconfigs/n/NCO/NCO-4.7.4-foss-2017b.eb new file mode 100644 index 00000000000..6ff3ca1db48 --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-4.7.4-foss-2017b.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'NCO' +version = '4.7.4' + +homepage = "http://nco.sourceforge.net" +description = """manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['http://nco.sourceforge.net/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c9848ebb5f32ff6d74ba44906b226023fd9073a31bc40e719b1b71728d648632'] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('UDUNITS', '2.2.25'), + ('expat', '2.2.4'), + ('ANTLR', '2.7.7'), + ('libdap', '3.19.1'), + ('GSL', '2.4'), + # sticking to netCDF 4.4.1.1 with HDF5 1.8.19 for compatibility with ESMF + ('netCDF', '4.4.1.1', '-HDF5-1.8.19'), +] + +sanity_check_paths = { + 'files': ['bin/nc%s' % x for x in ('ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', + 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/NetPIPE/NetPIPE-5.1-intel-2018a.eb b/easybuild/easyconfigs/n/NetPIPE/NetPIPE-5.1-intel-2018a.eb new file mode 100644 index 00000000000..8cd00165bb1 --- /dev/null +++ b/easybuild/easyconfigs/n/NetPIPE/NetPIPE-5.1-intel-2018a.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'NetPIPE' +version = '5.1' + +homepage = 'http://netpipe.cs.ksu.edu/' +description = """NetPIPE is a protocol independent communication performance benchmark that visually represents + the network performance under a variety of conditions.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['http://netpipe.cs.ksu.edu/download/'] +sources = ['NetPIPE-%(version)s.tar.gz'] +checksums = ['0b6e6fd90446d06b70f0e615c56698887d3bb90b8a6be5d6d8a0ccb7efcd7b0b'] + +common_buildopts = 'CC="$CC" CFLAGS="$CFLAGS -lrt"' + +# possible values: disk, ibverbs, memcpy, mpi, shmem, tcp, theo +# shmem requires shmem.h (must be provided by OS?) +buildopts = [ + 'disk ' + common_buildopts, + 'ibverbs ' + common_buildopts, + 'memcpy ' + common_buildopts, + 'mpi ' + common_buildopts, + 'tcp ' + common_buildopts, + 'theo ' + common_buildopts, +] + +files_to_copy = [(['NP*'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/NPdisk', 'bin/NPibverbs', 'bin/NPmemcpy', 'bin/NPmpi', 'bin/NPtcp', 'bin/NPtheo'], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.2.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.2.1-intel-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..fbfdc193958 --- /dev/null +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.2.1-intel-2018a-Python-3.6.4.eb @@ -0,0 +1,47 @@ +easyblock = 'Bundle' + +name = 'NiBabel' +version = '2.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://nipy.github.io/nibabel' +description = """NiBabel provides read/write access to some common medical and neuroimaging file formats, + including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT + as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and + annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +dependencies = [ + ('Python', '3.6.4'), + ('Pillow', '5.0.0', versionsuffix), +] + +# raise an error when auto-downloading of dependency packages is detected +exts_download_dep_fail = True + +exts_defaultclass = 'PythonPackage' +exts_list = [ + ('pydicom', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pydicom'], + 'start_dir': 'source', + 'checksums': ['26988f7b38456702d18468642d06e710a68efd0ca281e3c410910b7b03205264'], + }), + (name, version, { + 'source_tmpl': 'nibabel-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/n/nibabel'], + 'checksums': ['a857cb6c0b55bd1f812314f0eab11956b48ab435310e44e75c52cf020d0aad98'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/nib-dicomfs', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/nibabel', 'lib/python%(pyshortver)s/site-packages/nisext'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/Nipype/Nipype-1.0.2-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/n/Nipype/Nipype-1.0.2-intel-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..d04fec6f197 --- /dev/null +++ b/easybuild/easyconfigs/n/Nipype/Nipype-1.0.2-intel-2018a-Python-3.6.4.eb @@ -0,0 +1,113 @@ +easyblock = 'Bundle' + +name = 'Nipype' +version = '1.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://nipy.org/nipype' +description = """Nipype is a Python project that provides a uniform interface to existing neuroimaging software and + facilitates interaction between these packages within a single workflow.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +dependencies = [ + ('Python', '3.6.4'), + ('lxml', '4.2.0', versionsuffix), + ('NiBabel', '2.2.1', versionsuffix), +] + +# raise an error when auto-downloading of dependency packages is detected +exts_download_dep_fail = True + +exts_defaultclass = 'PythonPackage' +exts_list = [ + ('networkx', '2.1', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], + 'checksums': ['64272ca418972b70a196cb15d9c85a5a6041f09a2f32e0d30c0255f25d458bb1'], + }), + ('traits', '4.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traits'], + 'checksums': ['5d82345e0a34b88e394964eea1be47419530027aef7f0b20ad315b6ec6c68370'], + }), + ('future', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/f/future'], + 'checksums': ['e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb'], + }), + ('packaging', '17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/packaging'], + 'checksums': ['f019b770dd64e585a99714f1fd5e01c7a8f11b45635aa953fd41c689a657375b'], + }), + ('pydot', '1.2.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pydot'], + 'checksums': ['92d2e2d15531d00710f2d6fb5540d2acabc5399d464f2f20d5d21073af241eb6'], + }), + ('pydotplus', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pydotplus'], + 'checksums': ['91e85e9ee9b85d2391ead7d635e3d9c7f5f44fd60a60e59b13e2403fa66505c4'], + }), + ('pluggy', '0.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy'], + 'checksums': ['7f8ae7f5bdf75671a718d2daf0a64b7885f74510bcd98b1a0bb420eb9a9d0cff'], + }), + ('more-itertools', '4.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools'], + 'checksums': ['c9ce7eccdcb901a2c75d326ea134e0886abfbea5f93e91cc95de9507c0816c44'], + 'modulename': 'more_itertools', + }), + ('attrs', '17.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/attrs'], + 'checksums': ['1c7960ccfd6a005cd9f7ba884e6316b5e430a3f1a6c37c5f87d8b43f83b54ec9'], + 'modulename': 'attr', + }), + ('py', '1.5.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py'], + 'checksums': ['29c9fab495d7528e80ba1e343b958684f4ace687327e6f789a94bf3d1915f881'], + }), + ('pytest', '3.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytest'], + 'checksums': ['54713b26c97538db6ff0703a12b19aeaeb60b5e599de542e7fca0ec83b9038e8'], + }), + ('funcsigs', version, { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('click', '6.7', { + 'source_urls': ['https://pypi.python.org/packages/source/c/click'], + 'checksums': ['f15516df478d5a56180fbf80e68f206010e6d160fc39fa508b65e035fd75130b'], + }), + ('isodate', '0.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/isodate'], + 'checksums': ['2e364a3d5759479cdb2d37cce6b9376ea504db2ff90252a2e5b7cc89cc9ff2d8'], + }), + ('rdflib', '4.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/r/rdflib'], + 'checksums': ['da1df14552555c5c7715d8ce71c08f404c988c58a1ecd38552d0da4fc261280d'], + }), + ('prov', '1.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/prov'], + 'checksums': ['96a74efa1b3324961ff66246539ed7bdc06245dcbeef538688c755a0ad5777ee'], + }), + ('simplejson', '3.14.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson'], + 'checksums': ['1ebbd84c2d7512f7ba65df0b9cc3cbc1bbd6ef9eab39fc9389dfe7e3681f7bd2'], + }), + ('nipype', version, { + 'source_urls': ['https://pypi.python.org/packages/source/n/nipype'], + 'checksums': ['1ed65f3e97fd0f82c418ad48af2107050e86d9e39eea4d22381ad7df932bf1ec'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/nipypecli'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'import nipype.interfaces'"] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/ncview/ncview-2.1.7-foss-2017b.eb b/easybuild/easyconfigs/n/ncview/ncview-2.1.7-foss-2017b.eb new file mode 100644 index 00000000000..723be518824 --- /dev/null +++ b/easybuild/easyconfigs/n/ncview/ncview-2.1.7-foss-2017b.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +## +easyblock = 'ConfigureMake' + +name = 'ncview' +version = '2.1.7' + +homepage = 'http://meteora.ucsd.edu/~pierce/ncview_home_page.html' +description = """Ncview is a visual browser for netCDF format files. +Typically you would use ncview to get a quick and easy, push-button +look at your netCDF files. You can view simple movies of the data, +view along various dimensions, take a look at the actual data values, +change color maps, invert the data, etc.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['ftp://cirrus.ucsd.edu/pub/ncview/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a14c2dddac0fc78dad9e4e7e35e2119562589738f4ded55ff6e0eca04d682c82'] + +# specified compiler is hard checked against (full path to) compiler used for netCDF... +preconfigopts = "CC=$(which $CC) " +configopts = "--with-udunits2_incdir=$EBROOTUDUNITS/include --with-udunits2_libdir=$EBROOTUDUNITS/lib " +configopts += "--with-nc-config=$EBROOTNETCDF/bin/nc-config" + +dependencies = [ + ('netCDF', '4.4.1.1', '-HDF5-1.8.19'), + ('netCDF-Fortran', '4.4.4', '-HDF5-1.8.19'), + ('UDUNITS', '2.2.25'), + ('X11', '20171023'), + ('libpng', '1.6.32'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/ncview'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-foss-2017b-HDF5-1.8.19.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-foss-2017b-HDF5-1.8.19.eb new file mode 100644 index 00000000000..66e694ebcb5 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-foss-2017b-HDF5-1.8.19.eb @@ -0,0 +1,19 @@ +name = 'netCDF-Fortran' +version = '4.4.4' +versionsuffix = '-HDF5-1.8.19' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['44b1986c427989604df9925dcdbf6c1a977e4ecbde6dd459114bca20bf5e9e67'] + +dependencies = [('netCDF', '4.4.1.1', versionsuffix)] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-foss-2017b-HDF5-1.8.19.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-foss-2017b-HDF5-1.8.19.eb new file mode 100644 index 00000000000..f27622e9ac2 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-foss-2017b-HDF5-1.8.19.eb @@ -0,0 +1,36 @@ +name = 'netCDF' +version = '4.4.1.1' +hdf5_ver = '1.8.19' +versionsuffix = '-HDF5-%s' % hdf5_ver + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7f040a0542ed3f6d27f3002b074e509614e18d6c515b2005d1537fec01b24909'] + +dependencies = [ + ('HDF5', hdf5_ver), + ('cURL', '7.56.0'), + ('Szip', '2.1.1'), +] + +builddependencies = [ + ('Autotools', '20170619'), + ('CMake', '3.9.4'), + ('Doxygen', '1.8.13'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.0-foss-2017b-Python-3.6.2-HDF5-1.8.19.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.0-foss-2017b-Python-3.6.2-HDF5-1.8.19.eb new file mode 100644 index 00000000000..ce1b794f025 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.0-foss-2017b-Python-3.6.2-HDF5-1.8.19.eb @@ -0,0 +1,26 @@ +name = 'netcdf4-python' +version = '1.4.0' +versionsuffix = '-Python-%(pyver)s-HDF5-1.8.19' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf4-python/archive/'] +sources = ['v%(version)srel.tar.gz'] +patches = ['netcdf4-python-1.1.8-avoid-diskless-test.patch'] +checksums = [ + 'cbb6d58a7182821d6dd52a52042de772c2d342731800b4704323d12233f3ff1a', + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', +] + +dependencies = [ + ('Python', '3.6.2'), + ('cftime', '1.0.0b1', '-Python-%(pyver)s'), + ('netCDF', '4.4.1.1', '-HDF5-1.8.19'), + ('cURL', '7.56.0'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.0-intel-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..4bb255bfa66 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.0-intel-2018a-Python-3.6.4.eb @@ -0,0 +1,27 @@ +name = 'netcdf4-python' +version = '1.4.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf4-python/archive/'] +sources = ['v%(version)srel.tar.gz'] +patches = ['netcdf4-python-1.1.8-avoid-diskless-test.patch'] +checksums = [ + 'cbb6d58a7182821d6dd52a52042de772c2d342731800b4704323d12233f3ff1a', # v1.4.0rel.tar.gz + # netcdf4-python-1.1.8-avoid-diskless-test.patch + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', +] + +dependencies = [ + ('Python', '3.6.4'), + ('cftime', '1.0.0', '-Python-%(pyver)s'), + ('netCDF', '4.6.0'), + ('cURL', '7.58.0'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.6.4-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.6.4-foss-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..e3e4677b74c --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.6.4-foss-2018a-Python-3.6.4.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'numexpr' +version = '2.6.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://code.google.com/p/numexpr/' +description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. + It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into + code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a + compiler at runtime.""" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = ['https://github.com/pydata/numexpr/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['049da1c07bd62d2aba29887130ccc9aff9b90962cb779a7b7ddc15e580368fba'] + +dependencies = [ + ('Python', '3.6.4'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-7.2.0-2.29.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-7.2.0-2.29.eb new file mode 100644 index 00000000000..86b86542660 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-7.2.0-2.29.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.20' + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'GCC', 'version': '7.2.0-2.29'} + +large_src = 'large.tgz' +timing_src = 'timing.tgz' + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'http://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +checksums = [ + '5ef38b15d9c652985774869efd548b8e3e972e1e99475c673b25537ed7bcf394', # v0.2.20.tar.gz (OpenBLAS) + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + # OpenBLAS-0.2.20_fix-Intel-L1-cache-size-detection.patch + '1d043e4838ec1f90b2b49318b780e3ab13b46133cb72a8d83eb0e3b1b056c4d6', + '1e6a046ab658c6e0b351de901d2812db28c2042f9f141416144c2faaf71fbb37', # OpenBLAS-0.2.20_revert-honor-cpuset.patch +] + +patches = [ + (large_src, '.'), + (timing_src, '.'), + 'OpenBLAS-%(version)s_fix-Intel-L1-cache-size-detection.patch', + 'OpenBLAS-%(version)s_revert-honor-cpuset.patch', +] + +skipsteps = ['configure'] + +buildopts = 'BINARY=64 USE_THREAD=1 USE_OPENMP=1 CC="$CC" FC="$F77"' +installopts = "USE_THREAD=1 USE_OPENMP=1 PREFIX=%(installdir)s" + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..a7338b7c2ce --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-6.4.0-2.28.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.3.0' + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} + +large_src = 'large.tgz' +timing_src = 'timing.tgz' + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'http://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +patches = [ + (large_src, '.'), + (timing_src, '.'), +] +checksums = [ + 'cf51543709abe364d8ecfb5c09a2b533d2b725ea1a66f203509b21a8e9d8f1a1', # v0.3.0.tar.gz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] + +skipsteps = ['configure'] + +buildopts = 'BINARY=64 USE_THREAD=1 USE_OPENMP=1 CC="$CC" FC="$F77"' +installopts = "USE_THREAD=1 USE_OPENMP=1 PREFIX=%(installdir)s" + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-5.0-20180108-intel-2018a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-5.0-20180108-intel-2018a.eb new file mode 100644 index 00000000000..43823062d9d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-5.0-20180108-intel-2018a.eb @@ -0,0 +1,45 @@ +name = 'OpenFOAM' +# bugfix release of OpenFOAM 5.0, see also https://openfoam.org/news/v5-0-patch/ +# https://github.com/OpenFOAM/OpenFOAM-5.x/commit/c409ae7d90966250bb3be9cfbc2a0538bc8e288d +version = '5.0-20180108' +commit = 'c409ae7' + +homepage = 'http://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s.x/archive'] +sources = [{'download_filename': '%s.tar.gz' % commit, 'filename': SOURCE_TAR_GZ}] +patches = [ + 'OpenFOAM-%(version)s_cleanup.patch', + 'OpenFOAM-%(version)s_fix-decomposedBlockData.patch', +] +checksums = [ + 'bc805137ce65674c9067257ab239e1f2f820b12edfaf40a4d7c6de260dc6ad25', # OpenFOAM-5.0-20180108.tar.gz + 'f5768f5dbc422fc2f4183fd288dc6afb2370115384f3e8b9b0e155c943868989', # OpenFOAM-5.0-20180108_cleanup.patch + # OpenFOAM-5.0-20180108_fix-decomposedBlockData.patch + '62c1585a43503c7550355ec6417fbfd28c22e750f559eaf72785d2bb630a4005', +] + +dependencies = [ + ('libreadline', '7.0'), + ('ncurses', '6.0'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.0.5'), + ('CGAL', '4.11.1', '-Python-2.7.14'), + ('ParaView', '5.4.1', '-mpi'), +] + +builddependencies = [ + ('CMake', '3.10.2'), + ('Bison', '3.0.4'), + ('flex', '2.6.4'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.6.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.6.0-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..7b9344076f3 --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.6.0-GCCcore-6.4.0.eb @@ -0,0 +1,55 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '5.6.0' + +homepage = 'http://icl.cs.utk.edu/projects/papi/' + +description = """ + PAPI provides the tool designer and application engineer with a consistent + interface and methodology for use of the performance counter hardware found + in most major microprocessors. PAPI enables software engineers to see, in near + real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and + software stack. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://icl.cs.utk.edu/projects/papi/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['49b7293f9ca2d74d6d80bd06b5c4be303663123267b4ac0884cbcae4c914dc47'] + +builddependencies = [ + ('binutils', '2.28'), +] + +start_dir = 'src' + +parallel = 1 + +runtest = 'fulltest' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x + for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", + "version", "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.8.3-foss-2017b-downloaded-deps.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.8.3-foss-2017b-downloaded-deps.eb new file mode 100644 index 00000000000..1d467e5ef31 --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.8.3-foss-2017b-downloaded-deps.eb @@ -0,0 +1,30 @@ +name = 'PETSc' +version = '3.8.3' +versionsuffix = '-downloaded-deps' + +homepage = 'http://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['01f9c3ed937eafac6c9e006510b61c7cd07197115ec40c429fc835f346ca3eac'] + +# (build) dependencies provided through EasyBuild +builddependencies = [('CMake', '3.9.5')] +dependencies = [('HDF5', '1.10.1')] + +# external packages that are downloaded with --download-=1 and --download--static=1 +download_deps_static = ['hypre', 'metis', 'ml', 'mumps', 'parmetis', 'prometheus', 'ptscotch', 'suitesparse', + 'superlu', 'superlu_dist'] +# triangle cannot be downloaded with --download-triangle-static because it fails +download_deps = ['triangle'] + +configopts = "--with-hdf5=1 --with-hdf5-dir=$EBROOTHDF5" + +shared_libs = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.9.1-foss-2018a-downloaded-deps.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.9.1-foss-2018a-downloaded-deps.eb new file mode 100644 index 00000000000..a1649295d9a --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.9.1-foss-2018a-downloaded-deps.eb @@ -0,0 +1,38 @@ +name = 'PETSc' +version = '3.9.1' +versionsuffix = '-downloaded-deps' + +homepage = 'http://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'foss', 'version': '2018a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['742e838a35d278693e956ed1ca4592c1d663451f6beea0694bf334aeb67681e8'] + +# (build) dependencies provided through EasyBuild +builddependencies = [ + ('CMake', '3.11.1'), + ('flex', '2.6.4'), + ('Bison', '3.0.4'), +] +dependencies = [ + ('HDF5', '1.10.1'), + ('Valgrind', '3.13.0'), +] + +# external packages that are downloaded with --download-=1 and --download--static=1 +download_deps_static = ['hypre', 'metis', 'ml', 'mumps', 'parmetis', 'prometheus', 'ptscotch', 'suitesparse', + 'superlu', 'superlu_dist'] + +# triangle cannot be downloaded with --download-triangle-static because it fails +download_deps = ['triangle'] + +configopts = "--with-hdf5=1 --with-hdf5-dir=$EBROOTHDF5 --with-debugging" + +shared_libs = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/PGI/PGI-18.4-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/p/PGI/PGI-18.4-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..7dbed209fb7 --- /dev/null +++ b/easybuild/easyconfigs/p/PGI/PGI-18.4-GCC-6.4.0-2.28.eb @@ -0,0 +1,25 @@ +name = 'PGI' +version = '18.4' + +homepage = 'http://www.pgroup.com/' +description = "C, C++ and Fortran compilers from The Portland Group - PGI" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86-64.tar.gz'] +checksums = ['81e0dcf6000b026093ece180d42d77854c23269fb8409cedcf51c674ca580a0f'] + +gccver = '6.4.0' +binutilsver = '2.28' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), + ('numactl', '2.0.11', '', ('GCCcore', gccver)), +] + +# license file +license_file = HOME + '/licenses/pgi/license.dat' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-170427-intel-2018a.eb b/easybuild/easyconfigs/p/PRANK/PRANK-170427-intel-2018a.eb new file mode 100644 index 00000000000..887083258fe --- /dev/null +++ b/easybuild/easyconfigs/p/PRANK/PRANK-170427-intel-2018a.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'PRANK' +version = '170427' + +homepage = 'http://wasabiapp.org/software/prank/' +description = """ PRANK is a probabilistic multiple alignment program for DNA, + codon and amino-acid sequences. PRANK is based on a novel algorithm that treats + insertions correctly and avoids over-estimation of the number of deletion events.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['http://wasabiapp.org/download/prank/'] +sources = ['%(namelower)s.source.%(version)s.tgz'] +checksums = ['623eb5e9b5cb0be1f49c3bf715e5fabceb1059b21168437264bdcd5c587a8859'] + +# PRANK uses MAFFT as external tool to contruct guide tree +dependencies = [('MAFFT', '7.397', '-with-extensions')] + +start_dir = 'src' + +files_to_copy = [(['prank'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/prank'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Pandoc/Pandoc-2.1.3.eb b/easybuild/easyconfigs/p/Pandoc/Pandoc-2.1.3.eb new file mode 100644 index 00000000000..5806fbc2abf --- /dev/null +++ b/easybuild/easyconfigs/p/Pandoc/Pandoc-2.1.3.eb @@ -0,0 +1,25 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Tarball' + +name = 'Pandoc' +version = '2.1.3' + +homepage = 'http://pandoc.org' +description = "If you need to convert files from one markup format into another, pandoc is your swiss-army knife" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/jgm/pandoc/releases/download/%(version)s/'] +sources = ['%(name)s-%(version)s-linux.tar.gz'] +checksums = ['829f7022b6bf5164ad5aabb88ad18d432e2ed15b11625d14ca76eee476c16a2d'] + +sanity_check_paths = { + 'files': ['bin/pandoc', 'bin/pandoc-citeproc'], + 'dirs': ['share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.4.1-intel-2018a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.4.1-intel-2018a-mpi.eb new file mode 100644 index 00000000000..a5c5e52d921 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.4.1-intel-2018a-mpi.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.4.1' +versionsuffix = '-mpi' + +homepage = "http://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'pic': True, 'usempi': True} + +download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] +sources = ["ParaView-v%(version)s.tar.gz"] +checksums = ['390d0f5dc66bf432e202a39b1f34193af4bf8aad2355338fa5e2778ea07a80e4'] + +dependencies = [ + ('X11', '20180131'), + ('Mesa', '17.3.6'), + ('libGLU', '9.0.0'), + ('Qt', '4.8.7'), + ('zlib', '1.2.11'), + ('HDF5', '1.10.1'), + ('Python', '2.7.14'), +] + +builddependencies = [('CMake', '3.10.2')] + +separate_build_dir = True + +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON ' +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s ' % SHLIB_EXT +configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.%s ' % SHLIB_EXT +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT +configopts += '-DVTK_USE_SYSTEM_HDF5=ON -DPARAVIEW_ENABLE_PYTHON=ON -DBUILD_SHARED_LIBS=ON ' +# if you want to build server only Paraview, uncomment the following line: +# configopts += '-DVTK_USE_X=OFF ' + +# Without internet connection turn off testing (uncomment the following line) +configopts += '-DBUILD_TESTING=OFF ' +# Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md +# and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly +# Without internet connection, comment the following two lines (configopts and prebuildopts) +configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' + +configopts += ' -DPARAVIEW_QT_VERSION=4 -DQT_QMAKE_EXECUTABLE=$EBROOTQT/bin/qmake ' +# The ParaView server can be cranky, test downloads are quite often failing, especially in the case +# of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +# first serial attempt would fail. +prebuildopts = 'make VTKData ;' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.26.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.26.1-GCCcore-6.4.0.eb index 2cc970473a1..e8316deef61 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.26.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.26.1-GCCcore-6.4.0.eb @@ -1148,9 +1148,235 @@ exts_list = [ }), ('Math::CDF', '0.1', { 'source_tmpl': 'Math-CDF-%(version)s.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CA/CALLAHAN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CALLAHAN'], 'checksums': ['7896bf250835ce47dcc813cb8cf9dc576c5455de42e822dcd7d8d3fef2125565'], }), + ('Array::Utils', '0.5', { + 'source_tmpl': 'Array-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZM/ZMIJ/Array'], + 'checksums': ['89dd1b7fcd9b4379492a3a77496e39fe6cd379b773fd03a6b160dd26ede63770'], + }), + ('File::Grep', '0.02', { + 'source_tmpl': 'File-Grep-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MN/MNEYLON'], + 'checksums': ['462e15274eb6278521407ea302d9eea7252cd44cab2382871f7de833d5f85632'], + }), + ('File::Path', '2.15', { + 'source_tmpl': 'File-Path-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN'], + 'checksums': ['1570f3c1cdf93c50f65c2072e8f20ee121550771dfb7f6e563f503a2a7050744'], + }), + ('File::Slurper', '0.012', { + 'source_tmpl': 'File-Slurper-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['4efb2ea416b110a1bda6f8133549cc6ea3676402e3caf7529fce0313250aa578'], + }), + ('File::Temp', '0.2304', { + 'source_tmpl': 'File-Temp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['13415323e48f7c9f34efdedf3d35141a7c3435e2beb8c6b922229dc317d321ac'], + }), + ('Graph', '0.9704', { + 'source_tmpl': 'Graph-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JH/JHI'], + 'checksums': ['325e8eb07be2d09a909e450c13d3a42dcb2a2e96cc3ac780fe4572a0d80b2a25'], + }), + ('Graph::ReadWrite', '2.09', { + 'source_tmpl': 'Graph-ReadWrite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['b01ef06ce922eea12d5ce614d63ddc5f3ee7ad0d05f9577051d3f87a89799a4a'], + }), + ('Scalar::List::Utils', '1.50', { + 'modulename': 'List::Util', + 'source_tmpl': 'Scalar-List-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': ['06aab9c693380190e53be09be7daed20c5d6278f71956989c24cca7782013675'], + }), + ('PerlIO::utf8_strict', '0.007', { + 'source_tmpl': 'PerlIO-utf8_strict-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['83a33f2fe046cb3ad6afc80790635a423e2c7c6854afacc6998cd46951cc81cb'], + }), + ('Devel::OverloadInfo', '0.005', { + 'source_tmpl': 'Devel-OverloadInfo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILMARI'], + 'checksums': ['8bfde2ffa47c9946f8adc8cfc445c2f97b8d1cdd678111bee9f444e82f7aa6e7'], + }), + ('Sub::Identify', '0.14', { + 'source_tmpl': 'Sub-Identify-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RG/RGARCIA'], + 'checksums': ['068d272086514dd1e842b6a40b1bedbafee63900e5b08890ef6700039defad6f'], + }), + ('Digest::MD5::File', '0.08', { + 'source_tmpl': 'Digest-MD5-File-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + 'checksums': ['adb43a54e32627b4f7e57c9640e6eb06d0bb79d8ea54cd0bd79ed35688fb1218'], + }), + ('String::RewritePrefix', '0.007', { + 'source_tmpl': 'String-RewritePrefix-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['5cbbccd5636315a90ddec3610c718411b971ae4b74d5e9e2c9a0b3f976a0dda2'], + }), + ('Getopt::Long::Descriptive', '0.102', { + 'source_tmpl': 'Getopt-Long-Descriptive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['9ad4b98f294aa0515cc3150a1ae878d39e470762b78d8bd9df055eba9dea2846'], + }), + ('App::Cmd', '0.331', { + 'source_tmpl': 'App-Cmd-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['4a5d3df0006bd278880d01f4957aaa652a8f91fe8f66e93adf70fba0c3ecb680'], + }), + ('Path::Tiny', '0.104', { + 'source_tmpl': 'Path-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['c69f1dcfeb4aa004086deb9bc14c7d79f45798b947f1efbd634a3442e267aaef'], + }), + ('Carp::Clan', '6.06', { + 'source_tmpl': 'Carp-Clan-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'], + 'checksums': ['ea4ac8f611354756d43cb369880032901e9cc4cc7e0bebb7b647186dac00c9d4'], + }), + ('Sub::Exporter::ForMethods', '0.100052', { + 'source_tmpl': 'Sub-Exporter-ForMethods-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['421fbba4f6ffcf13c4335f2c20630d709e6fa659c07545d094dbc5a558ad3006'], + }), + ('MooseX::Types', '0.50', { + 'source_tmpl': 'MooseX-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['9cd87b3492cbf0be9d2df9317b2adf9fc30663770e69906654bea3f41b17cb08'], + }), + ('B::Hooks::EndOfScope', '0.24', { + 'source_tmpl': 'B-Hooks-EndOfScope-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['03aa3dfe5d0aa6471a96f43fe8318179d19794d4a640708f0288f9216ec7acc6'], + }), + ('namespace::clean', '0.27', { + 'source_tmpl': 'namespace-clean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], + 'checksums': ['8a10a83c3e183dc78f9e7b7aa4d09b47c11fb4e7d3a33b9a12912fd22e31af9d'], + }), + ('namespace::autoclean', '0.28', { + 'source_tmpl': 'namespace-autoclean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['cd410a1681add521a28805da2e138d44f0d542407b50999252a147e553c26c39'], + }), + ('File::pushd', '1.014', { + 'source_tmpl': 'File-pushd-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['b5ab37ffe3acbec53efb7c77b4423a2c79afa30a48298e751b9ebee3fdc6340b'], + }), + ('MooseX::Types::Perl', '0.101343', { + 'source_tmpl': 'MooseX-Types-Perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['f084beaf3c33209c68d05d4dbc24c25d604a6458b9738d96dceb086c8ef1325a'], + }), + ('Role::Tiny', '2.000006', { + 'source_tmpl': 'Role-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['cc73418c904a0286ecd8915eac11f5be2a8d1e17ea9cb54c9116b0340cd3e382'], + }), + ('Specio', '0.42', { + 'source_tmpl': 'Specio-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['23298b93a26d7ae3c1d58106f5898d84ddc71b626afdbf801bddb04d5e524ef6'], + }), + ('Params::ValidationCompiler', '0.27', { + 'source_tmpl': 'Params-ValidationCompiler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['50a99968359d430e34ea8a12e7f08a669ffd34a3dae4d8ea9ca076c1100af9b2'], + }), + ('Log::Dispatch', '2.67', { + 'source_tmpl': 'Log-Dispatch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['a94da2a5a24b3519012b69b94d32c558b332fae1a37c773e6e058009e2d0f304'], + }), + ('String::Flogger', '1.101245', { + 'source_tmpl': 'String-Flogger-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['aa03c08e01f802a358c175c6093c02adf9688659a087a8ddefdc3e9cef72640b'], + }), + ('Log::Dispatchouli', '2.016', { + 'source_tmpl': 'Log-Dispatchouli-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['7f2a1a1854fd1e4ed02883bc21f5395f4244a266b661276b438d1bdd50bdacf7'], + }), + ('Data::Section', '0.200007', { + 'source_tmpl': 'Data-Section-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['cd937e5b70e34aab885ff414e2a6d19e4783b7c28fc3cda5145b230514ebb4de'], + }), + ('Software::License', '0.103013', { + 'source_tmpl': 'Software-License-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['2641d937390f43b08fa31c419713cd96a2f0bf160be04cab322631daf6810ff3'], + }), + ('MooseX::SetOnce', '0.200002', { + 'source_tmpl': 'MooseX-SetOnce-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['cbed06b7fcd353f0d99bf80a87c1c0b581160697231b3ad9a608da231ba2b659'], + }), + ('Term::Encoding', '0.02', { + 'source_tmpl': 'Term-Encoding-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['f274e72346a0c0cfacfb53030ac1e38b57425512fc5bdc5cd9ef75ab0f26cfcc'], + }), + ('Config::MVP', '2.200011', { + 'source_tmpl': 'Config-MVP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['23c95666fc43c4adaebcc093b1b56091efc2a6aa2d75366a216d18eda96ad716'], + }), + ('Throwable', '0.200013', { + 'source_tmpl': 'Throwable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['9987d0deb5bddd352a6330cefbe932f882e36dd8c8a4564bcfd372dc396b8fa0'], + }), + ('Sub::Quote', '2.005001', { + 'source_tmpl': 'Sub-Quote-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['d6ab4f0775def015367a05e02024b403f991b2be11d774f3d235fe7e9bdbba07'], + }), + ('Role::Identifiable::HasIdent', '0.007', { + 'source_tmpl': 'Role-Identifiable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['561346d1a1a07a45bd851d859a825a7f67925a7a3ba5ba58e0cdad8bb99073ad'], + }), + ('Role::HasMessage', '0.006', { + 'source_tmpl': 'Role-HasMessage-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['f6a6dbe0476ff95ee1ffbef825eb18d9b02b0618deba4686e7c63b99d576d4d3'], + }), + ('MooseX::OneArgNew', '0.005', { + 'source_tmpl': 'MooseX-OneArgNew-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['7e4fcf474ea6c4244f0885f1066729cfdc472fbd7190dd41b4b55bcd67c3103f'], + }), + ('MooseX::Role::Parameterized', '1.10', { + 'source_tmpl': 'MooseX-Role-Parameterized-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['4846c12f7cd304419c983eb3654d303462d06a3a5f941e21c76957806c119d5e'], + }), + ('MooseX::LazyRequire', '0.11', { + 'source_tmpl': 'MooseX-LazyRequire-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['ef620c1e019daf9cf3f23a943d25a94c91e93ab312bcd63be2e9740ec0b94288'], + }), + ('Mixin::Linewise::Readers', '0.108', { + 'source_tmpl': 'Mixin-Linewise-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['7df20678474c0973930a472b0c55e3f8e85b7790b68ab18ef618f9c453c8aef2'], + }), + ('Config::INI', '0.025', { + 'source_tmpl': 'Config-INI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['628bf76d5b91f89dde22d4813ec033026ebf71b772bb61ccda909da00c869732'], + }), + ('Dist::Zilla', '6.012', { + 'source_tmpl': 'Dist-Zilla-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['67583075f6d62b78aaa956389f113df789ddd41911394092a5a2b8c6fa863070'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.26.1-foss-2018a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.26.1-foss-2018a.eb index e15cf500685..d43c77f2fc2 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.26.1-foss-2018a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.26.1-foss-2018a.eb @@ -1146,9 +1146,235 @@ exts_list = [ }), ('Math::CDF', '0.1', { 'source_tmpl': 'Math-CDF-%(version)s.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CA/CALLAHAN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CALLAHAN'], 'checksums': ['7896bf250835ce47dcc813cb8cf9dc576c5455de42e822dcd7d8d3fef2125565'], }), + ('Array::Utils', '0.5', { + 'source_tmpl': 'Array-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZM/ZMIJ/Array'], + 'checksums': ['89dd1b7fcd9b4379492a3a77496e39fe6cd379b773fd03a6b160dd26ede63770'], + }), + ('File::Grep', '0.02', { + 'source_tmpl': 'File-Grep-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MN/MNEYLON'], + 'checksums': ['462e15274eb6278521407ea302d9eea7252cd44cab2382871f7de833d5f85632'], + }), + ('File::Path', '2.15', { + 'source_tmpl': 'File-Path-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN'], + 'checksums': ['1570f3c1cdf93c50f65c2072e8f20ee121550771dfb7f6e563f503a2a7050744'], + }), + ('File::Slurper', '0.012', { + 'source_tmpl': 'File-Slurper-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['4efb2ea416b110a1bda6f8133549cc6ea3676402e3caf7529fce0313250aa578'], + }), + ('File::Temp', '0.2304', { + 'source_tmpl': 'File-Temp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['13415323e48f7c9f34efdedf3d35141a7c3435e2beb8c6b922229dc317d321ac'], + }), + ('Graph', '0.9704', { + 'source_tmpl': 'Graph-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JH/JHI'], + 'checksums': ['325e8eb07be2d09a909e450c13d3a42dcb2a2e96cc3ac780fe4572a0d80b2a25'], + }), + ('Graph::ReadWrite', '2.09', { + 'source_tmpl': 'Graph-ReadWrite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['b01ef06ce922eea12d5ce614d63ddc5f3ee7ad0d05f9577051d3f87a89799a4a'], + }), + ('Scalar::List::Utils', '1.50', { + 'modulename': 'List::Util', + 'source_tmpl': 'Scalar-List-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': ['06aab9c693380190e53be09be7daed20c5d6278f71956989c24cca7782013675'], + }), + ('PerlIO::utf8_strict', '0.007', { + 'source_tmpl': 'PerlIO-utf8_strict-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['83a33f2fe046cb3ad6afc80790635a423e2c7c6854afacc6998cd46951cc81cb'], + }), + ('Devel::OverloadInfo', '0.005', { + 'source_tmpl': 'Devel-OverloadInfo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILMARI'], + 'checksums': ['8bfde2ffa47c9946f8adc8cfc445c2f97b8d1cdd678111bee9f444e82f7aa6e7'], + }), + ('Sub::Identify', '0.14', { + 'source_tmpl': 'Sub-Identify-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RG/RGARCIA'], + 'checksums': ['068d272086514dd1e842b6a40b1bedbafee63900e5b08890ef6700039defad6f'], + }), + ('Digest::MD5::File', '0.08', { + 'source_tmpl': 'Digest-MD5-File-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + 'checksums': ['adb43a54e32627b4f7e57c9640e6eb06d0bb79d8ea54cd0bd79ed35688fb1218'], + }), + ('String::RewritePrefix', '0.007', { + 'source_tmpl': 'String-RewritePrefix-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['5cbbccd5636315a90ddec3610c718411b971ae4b74d5e9e2c9a0b3f976a0dda2'], + }), + ('Getopt::Long::Descriptive', '0.102', { + 'source_tmpl': 'Getopt-Long-Descriptive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['9ad4b98f294aa0515cc3150a1ae878d39e470762b78d8bd9df055eba9dea2846'], + }), + ('App::Cmd', '0.331', { + 'source_tmpl': 'App-Cmd-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['4a5d3df0006bd278880d01f4957aaa652a8f91fe8f66e93adf70fba0c3ecb680'], + }), + ('Path::Tiny', '0.104', { + 'source_tmpl': 'Path-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['c69f1dcfeb4aa004086deb9bc14c7d79f45798b947f1efbd634a3442e267aaef'], + }), + ('Carp::Clan', '6.06', { + 'source_tmpl': 'Carp-Clan-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'], + 'checksums': ['ea4ac8f611354756d43cb369880032901e9cc4cc7e0bebb7b647186dac00c9d4'], + }), + ('Sub::Exporter::ForMethods', '0.100052', { + 'source_tmpl': 'Sub-Exporter-ForMethods-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['421fbba4f6ffcf13c4335f2c20630d709e6fa659c07545d094dbc5a558ad3006'], + }), + ('MooseX::Types', '0.50', { + 'source_tmpl': 'MooseX-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['9cd87b3492cbf0be9d2df9317b2adf9fc30663770e69906654bea3f41b17cb08'], + }), + ('B::Hooks::EndOfScope', '0.24', { + 'source_tmpl': 'B-Hooks-EndOfScope-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['03aa3dfe5d0aa6471a96f43fe8318179d19794d4a640708f0288f9216ec7acc6'], + }), + ('namespace::clean', '0.27', { + 'source_tmpl': 'namespace-clean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], + 'checksums': ['8a10a83c3e183dc78f9e7b7aa4d09b47c11fb4e7d3a33b9a12912fd22e31af9d'], + }), + ('namespace::autoclean', '0.28', { + 'source_tmpl': 'namespace-autoclean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['cd410a1681add521a28805da2e138d44f0d542407b50999252a147e553c26c39'], + }), + ('File::pushd', '1.014', { + 'source_tmpl': 'File-pushd-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['b5ab37ffe3acbec53efb7c77b4423a2c79afa30a48298e751b9ebee3fdc6340b'], + }), + ('MooseX::Types::Perl', '0.101343', { + 'source_tmpl': 'MooseX-Types-Perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['f084beaf3c33209c68d05d4dbc24c25d604a6458b9738d96dceb086c8ef1325a'], + }), + ('Role::Tiny', '2.000006', { + 'source_tmpl': 'Role-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['cc73418c904a0286ecd8915eac11f5be2a8d1e17ea9cb54c9116b0340cd3e382'], + }), + ('Specio', '0.42', { + 'source_tmpl': 'Specio-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['23298b93a26d7ae3c1d58106f5898d84ddc71b626afdbf801bddb04d5e524ef6'], + }), + ('Params::ValidationCompiler', '0.27', { + 'source_tmpl': 'Params-ValidationCompiler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['50a99968359d430e34ea8a12e7f08a669ffd34a3dae4d8ea9ca076c1100af9b2'], + }), + ('Log::Dispatch', '2.67', { + 'source_tmpl': 'Log-Dispatch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['a94da2a5a24b3519012b69b94d32c558b332fae1a37c773e6e058009e2d0f304'], + }), + ('String::Flogger', '1.101245', { + 'source_tmpl': 'String-Flogger-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['aa03c08e01f802a358c175c6093c02adf9688659a087a8ddefdc3e9cef72640b'], + }), + ('Log::Dispatchouli', '2.016', { + 'source_tmpl': 'Log-Dispatchouli-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['7f2a1a1854fd1e4ed02883bc21f5395f4244a266b661276b438d1bdd50bdacf7'], + }), + ('Data::Section', '0.200007', { + 'source_tmpl': 'Data-Section-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['cd937e5b70e34aab885ff414e2a6d19e4783b7c28fc3cda5145b230514ebb4de'], + }), + ('Software::License', '0.103013', { + 'source_tmpl': 'Software-License-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['2641d937390f43b08fa31c419713cd96a2f0bf160be04cab322631daf6810ff3'], + }), + ('MooseX::SetOnce', '0.200002', { + 'source_tmpl': 'MooseX-SetOnce-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['cbed06b7fcd353f0d99bf80a87c1c0b581160697231b3ad9a608da231ba2b659'], + }), + ('Term::Encoding', '0.02', { + 'source_tmpl': 'Term-Encoding-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['f274e72346a0c0cfacfb53030ac1e38b57425512fc5bdc5cd9ef75ab0f26cfcc'], + }), + ('Config::MVP', '2.200011', { + 'source_tmpl': 'Config-MVP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['23c95666fc43c4adaebcc093b1b56091efc2a6aa2d75366a216d18eda96ad716'], + }), + ('Throwable', '0.200013', { + 'source_tmpl': 'Throwable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['9987d0deb5bddd352a6330cefbe932f882e36dd8c8a4564bcfd372dc396b8fa0'], + }), + ('Sub::Quote', '2.005001', { + 'source_tmpl': 'Sub-Quote-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['d6ab4f0775def015367a05e02024b403f991b2be11d774f3d235fe7e9bdbba07'], + }), + ('Role::Identifiable::HasIdent', '0.007', { + 'source_tmpl': 'Role-Identifiable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['561346d1a1a07a45bd851d859a825a7f67925a7a3ba5ba58e0cdad8bb99073ad'], + }), + ('Role::HasMessage', '0.006', { + 'source_tmpl': 'Role-HasMessage-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['f6a6dbe0476ff95ee1ffbef825eb18d9b02b0618deba4686e7c63b99d576d4d3'], + }), + ('MooseX::OneArgNew', '0.005', { + 'source_tmpl': 'MooseX-OneArgNew-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['7e4fcf474ea6c4244f0885f1066729cfdc472fbd7190dd41b4b55bcd67c3103f'], + }), + ('MooseX::Role::Parameterized', '1.10', { + 'source_tmpl': 'MooseX-Role-Parameterized-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['4846c12f7cd304419c983eb3654d303462d06a3a5f941e21c76957806c119d5e'], + }), + ('MooseX::LazyRequire', '0.11', { + 'source_tmpl': 'MooseX-LazyRequire-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['ef620c1e019daf9cf3f23a943d25a94c91e93ab312bcd63be2e9740ec0b94288'], + }), + ('Mixin::Linewise::Readers', '0.108', { + 'source_tmpl': 'Mixin-Linewise-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['7df20678474c0973930a472b0c55e3f8e85b7790b68ab18ef618f9c453c8aef2'], + }), + ('Config::INI', '0.025', { + 'source_tmpl': 'Config-INI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['628bf76d5b91f89dde22d4813ec033026ebf71b772bb61ccda909da00c869732'], + }), + ('Dist::Zilla', '6.012', { + 'source_tmpl': 'Dist-Zilla-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['67583075f6d62b78aaa956389f113df789ddd41911394092a5a2b8c6fa863070'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..494b389bd5a --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '5.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['12f29d6c23424f704c66b5b68c02fe0b571504459605cfe36ab8158359b0e1bb'] + +dependencies = [ + ('Python', '2.7.14'), + ('libjpeg-turbo', '1.5.3'), + ('libpng', '1.6.34'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.0.9'), + ('freetype', '2.9') +] + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pisces/Pisces-5.2.7.47-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/Pisces/Pisces-5.2.7.47-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..f644421b96c --- /dev/null +++ b/easybuild/easyconfigs/p/Pisces/Pisces-5.2.7.47-GCCcore-6.4.0.eb @@ -0,0 +1,30 @@ +easyblock = 'Tarball' + +name = 'Pisces' +version = '5.2.7.47' + +homepage = 'https://github.com/Illumina/Pisces' +description = "Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows." + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['https://github.com/Illumina/Pisces/releases/download/v%(version)s/'] +sources = ['Pisces_%(version)s.tar.gz'] +checksums = ['69f8e2c08c09b9d75a346474305e5cc4adc4713b11f788398a516fa2ab7e834f'] + +# note: only works on recent OSs, required sufficiently recent glibc (2.14 or newer) +dependencies = [('dotNET-Core-Runtime', '2.0.7')] + +sanity_check_paths = { + 'files': ['libFileCompression.so', 'Pisces.dll'], + 'dirs': [], +} + +sanity_check_commands = ["dotnet $EBROOTPISCES/Pisces.dll --help"] + +modextrapaths = { + 'LD_LIBRARY_PATH': [], + 'PATH': [''], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Proteinortho/Proteinortho-5.16b-foss-2018a-Python-3.6.4-Perl-5.26.1.eb b/easybuild/easyconfigs/p/Proteinortho/Proteinortho-5.16b-foss-2018a-Python-3.6.4-Perl-5.26.1.eb new file mode 100644 index 00000000000..260c2b372d4 --- /dev/null +++ b/easybuild/easyconfigs/p/Proteinortho/Proteinortho-5.16b-foss-2018a-Python-3.6.4-Perl-5.26.1.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'Proteinortho' +version = '5.16b' +versionsuffix = '-Python-%(pyver)s-Perl-%(perlver)s' + +homepage = 'http://www.bioinf.uni-leipzig.de/Software/proteinortho/' +description = "Proteinortho is a tool to detect orthologous genes within different species." + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = ['http://www.bioinf.uni-leipzig.de/Software/proteinortho/'] +sources = ['proteinortho_v%(version)s_src.tar.gz'] +checksums = ['d220d4af5ffae8190eec462d8b6c941022ce2927391493b7741c6b7db96a80f2'] + +dependencies = [ + ('Perl', '5.26.1'), + ('Python', '3.6.4'), + ('BLAST+', '2.7.1'), +] + +files_to_copy = [ + (['proteinortho%(version_major)s_clustering', 'proteinortho%(version_major)s_tree', 'chk_test.pl', + 'po2tree.pl', 'proteinortho%(version_major)s_clean_edges2.pl', 'proteinortho%(version_major)s.pl', + 'proteinortho%(version_major)s_singletons.pl', 'ffadj_mcs.py'], 'bin'), + 'tools', 'manual.html', +] + +sanity_check_paths = { + 'files': ["bin/proteinortho%(version_major)s_clustering", "bin/proteinortho%(version_major)s_tree", + "bin/proteinortho%(version_major)s.pl"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.4.2-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.4.2-foss-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..69d2a712eb3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.4.2-foss-2018a-Python-3.6.4.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'PyTables' +version = '3.4.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as + relational or object oriented databases.""" + +toolchain = {'name': 'foss', 'version': '2018a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/PyTables/PyTables/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['pyTables-3.4.2-fix-libs.patch'] +checksums = [ + '629a0227bb2b315c5d97629073696609eaee41d0fc89e03f997412613cd46d3a', # v3.4.2.tar.gz + 'f34a05573e7843e67dab011bede8436074362041747c028b409fac9f599231a3', # pyTables-3.4.2-fix-libs.patch +] + +dependencies = [ + ('Python', '3.6.4'), + ('numexpr', '2.6.4', versionsuffix), + ('HDF5', '1.10.1'), + ('LZO', '2.10'), + ('Blosc', '1.14.2'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['pt2to3', 'ptdump', 'ptrepack']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-17.0.0-foss-2018a-Python-2.7.14-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-17.0.0-foss-2018a-Python-2.7.14-zmq4.eb new file mode 100644 index 00000000000..2f13ccedd89 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-17.0.0-foss-2018a-Python-2.7.14-zmq4.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '17.0.0' +zmqversion = '4.2.5' +versionsuffix = '-Python-%%(pyver)s-zmq%s' % zmqversion.split('.')[0] + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['0145ae59139b41f65e047a3a9ed11bbc36e37d5e96c64382fcdff911c4d8c3f0'] + +dependencies = [ + ('Python', '2.7.14'), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/zmq'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-17.0.0-foss-2018a-Python-3.6.4-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-17.0.0-foss-2018a-Python-3.6.4-zmq4.eb new file mode 100644 index 00000000000..b0c636a6347 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-17.0.0-foss-2018a-Python-3.6.4-zmq4.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '17.0.0' +zmqversion = '4.2.5' +versionsuffix = '-Python-%%(pyver)s-zmq%s' % zmqversion.split('.')[0] + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['0145ae59139b41f65e047a3a9ed11bbc36e37d5e96c64382fcdff911c4d8c3f0'] + +dependencies = [ + ('Python', '3.6.4'), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/zmq'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-foss-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..9962089f15d --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-foss-2018a-Python-3.6.4.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 0.9.1.4: +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Erich Birngruber +# Gregor Mendel Institute + +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.14.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d2bb40cd083c1357768e4683377f03471d160cfe8421136630bfa47f5adb3219'] + +dependencies = [ + ('Python', '3.6.4'), + ('ncurses', '6.0'), + ('cURL', '7.58.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.14-foss-2017b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.14-foss-2017b.eb index afc89bbd1b1..8b4bc66b401 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.14-foss-2017b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.14-foss-2017b.eb @@ -233,6 +233,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), + ('py_expression_eval', '0.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], + 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.14-foss-2018a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.14-foss-2018a.eb index 51bcb2de0c7..cf093361f8e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.14-foss-2018a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.14-foss-2018a.eb @@ -178,6 +178,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), + ('py_expression_eval', '0.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], + 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2017b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2017b.eb index 602e5928949..f0f5d16bf04 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2017b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2017b.eb @@ -233,6 +233,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), + ('py_expression_eval', '0.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], + 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2018.01.eb b/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2018.01.eb index 2679976c29b..54746e7181c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2018.01.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2018.01.eb @@ -232,6 +232,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), + ('py_expression_eval', '0.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], + 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2018a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2018a.eb index 109549b24bd..0918861898c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2018a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.14-intel-2018a.eb @@ -175,6 +175,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), + ('py_expression_eval', '0.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], + 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.14-iomkl-2018a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.14-iomkl-2018a.eb index 6b767c047c4..ff893beb3c6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.14-iomkl-2018a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.14-iomkl-2018a.eb @@ -175,6 +175,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), + ('py_expression_eval', '0.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], + 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.4-foss-2017a.eb b/easybuild/easyconfigs/p/Python/Python-3.6.4-foss-2017a.eb index 3fce57061a6..63a0be7a096 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.4-foss-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.4-foss-2017a.eb @@ -213,6 +213,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), + ('py_expression_eval', '0.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], + 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.4-foss-2018a.eb b/easybuild/easyconfigs/p/Python/Python-3.6.4-foss-2018a.eb index 23139aae8d6..972371a0d32 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.4-foss-2018a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.4-foss-2018a.eb @@ -208,6 +208,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), + ('py_expression_eval', '0.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], + 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.4-golf-2018a.eb b/easybuild/easyconfigs/p/Python/Python-3.6.4-golf-2018a.eb index f64f3d4a00f..82c7ba3871c 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.4-golf-2018a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.4-golf-2018a.eb @@ -204,6 +204,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), + ('py_expression_eval', '0.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], + 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.4-intel-2018a.eb b/easybuild/easyconfigs/p/Python/Python-3.6.4-intel-2018a.eb index 5a7e2e5ef40..4522b977baf 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.4-intel-2018a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.4-intel-2018a.eb @@ -212,6 +212,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), + ('py_expression_eval', '0.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], + 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.4-iomkl-2018a.eb b/easybuild/easyconfigs/p/Python/Python-3.6.4-iomkl-2018a.eb index fc052d2a39a..68a21ee0ab7 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.4-iomkl-2018a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.4-iomkl-2018a.eb @@ -171,6 +171,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], }), + ('py_expression_eval', '0.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], + 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/parallel/parallel-20180422-intel-2018a.eb b/easybuild/easyconfigs/p/parallel/parallel-20180422-intel-2018a.eb new file mode 100644 index 00000000000..f3ae5c25396 --- /dev/null +++ b/easybuild/easyconfigs/p/parallel/parallel-20180422-intel-2018a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'parallel' +version = '20180422' + +homepage = 'http://savannah.gnu.org/projects/parallel/' +description = """parallel: Build and execute shell commands in parallel""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['9dce21cac7d91bd84cef0da106182ad3c96ac18e012595df4981b4c7fbba4e77'] + +dependencies = [ + ('Perl', '5.26.1'), +] + +sanity_check_paths = { + 'files': ['bin/parallel'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pyshp/pyshp-1.2.12-foss-2017b-Python-3.6.2.eb b/easybuild/easyconfigs/p/pyshp/pyshp-1.2.12-foss-2017b-Python-3.6.2.eb new file mode 100644 index 00000000000..cbccbb80aea --- /dev/null +++ b/easybuild/easyconfigs/p/pyshp/pyshp-1.2.12-foss-2017b-Python-3.6.2.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'pyshp' +version = '1.2.12' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/GeospatialPython/pyshp' +description = """Pure Python read/write support for ESRI Shapefile format""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['https://github.com/GeospatialPython/pyshp/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['cf6514c0b6dd6addeea90efc9386e22c67f96f642cb6667542875591abcc3656'] + +dependencies = [ + ('Python', '3.6.2'), + ('cURL', '7.56.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'shapefile'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-4.6.3-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/q/QUAST/QUAST-4.6.3-foss-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..a1e5b1309f0 --- /dev/null +++ b/easybuild/easyconfigs/q/QUAST/QUAST-4.6.3-foss-2018a-Python-3.6.4.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonPackage' + +name = 'QUAST' +version = '4.6.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/ablab/%(namelower)s' +description = """QUAST evaluates genome assemblies by computing various metrics. + It works both with and without reference genomes. The tool accepts multiple + assemblies, thus is suitable for comparison.""" + +toolchain = {'name': 'foss', 'version': '2018a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/ablab/%(namelower)s/archive/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +checksums = ['d7f5e670563d17d683f6df057086f7b816b6a088266c6270f7114a1406aaab63'] + +install_target = 'install_full' + +dependencies = [ + ('Python', '3.6.4'), + ('Perl', '5.26.1'), + ('matplotlib', '2.1.2', versionsuffix), + ('Java', '1.8.0_162', '', True), + ('Boost', '1.66.0'), +] + +options = {'modulename': '%(namelower)s_libs'} + +libraries = ['bedtools', 'bwa', 'ca_utils', 'gage', 'genemark', 'genemark-es', 'glimmer', 'gnuplot', 'html_saver', + 'kronatools', 'manta0.29.6', 'MUMmer', 'ra_utils', 'sambamba', 'silva'] +sanity_check_paths = { + 'files': ['bin/%(namelower)s.py', 'bin/meta%(namelower)s.py'], + 'dirs': [('lib/python%%(pyshortver)s/site-packages/%%(namelower)s-%%(version)s-py%%(pyshortver)s.egg/' + '%%(namelower)s_libs/%s') % x for x in libraries] +} + +sanity_check_commands = [ + "wget quast.sf.net/test_data.tar.gz && " + "tar xzf test_data.tar.gz && " + "%(namelower)s.py --test && " + "rm ./test_data.tar.gz ./test_data -rf" +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2018a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2018a.eb new file mode 100644 index 00000000000..31d3d37f43d --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2018a.eb @@ -0,0 +1,32 @@ +name = 'Qt' +version = '4.8.7' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'cstd': 'gnu++98'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] +patches = ['Qt-%(version)s_phonon-export.patch'] +checksums = [ + 'e2882295097e47fe089f8ac741a95fef47e0a73a3f3cdf21b56990638f626ea0', # qt-everywhere-opensource-src-4.8.7.tar.gz + '3853c87c33695bfa57e207ffb0d94cb2565aa462eccdf44d2b2804fd44ecbad6', # Qt-4.8.7_phonon-export.patch +] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.54.3'), + ('libpng', '1.6.34'), + ('X11', '20180131'), + ('libGLU', '9.0.0'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.6-intel-2017b-R-3.4.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.6-intel-2017b-R-3.4.3.eb index 4096986159e..98bc5c1e699 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.6-intel-2017b-R-3.4.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.6-intel-2017b-R-3.4.3.eb @@ -18,8 +18,10 @@ dependencies = [ exts_default_options = { 'source_urls': [ 'https://bioconductor.org/packages/3.6/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.6/bioc/src/contrib/Archive/%(name)s', 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/', 'https://bioconductor.org/packages/3.6/data/experiment/src/contrib/', + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'https://cran.r-project.org/src/contrib/', # current version of packages 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages ], diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.6-intel-2018a-R-3.4.4.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.6-intel-2018a-R-3.4.4.eb index b2fad84ae31..079e4a59e0f 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.6-intel-2018a-R-3.4.4.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.6-intel-2018a-R-3.4.4.eb @@ -18,8 +18,10 @@ dependencies = [ exts_default_options = { 'source_urls': [ 'https://bioconductor.org/packages/3.6/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.6/bioc/src/contrib/Archive/%(name)s', 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/', 'https://bioconductor.org/packages/3.6/data/experiment/src/contrib/', + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'https://cran.r-project.org/src/contrib/', # current version of packages 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages ], diff --git a/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb b/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb index 8646bd09e93..f07ec56721a 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb @@ -41,6 +41,7 @@ dependencies = [ ('NLopt', '2.4.2'), # for nloptr ('FFTW', '3.3.6'), # for fftw ('libsndfile', '1.0.28'), # for seewave + ('ICU', '61.1'), # for rJava & gdsfmt # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons # ('OpenSSL', '1.0.2h'), @@ -488,7 +489,7 @@ exts_list = [ 'checksums': ['2557d5d59a45620ec9de340c2c25eec4cc478d3fc3f8b87979cf337c5bcfde11'], }), ('foreign', '0.8-69', { - 'checksums': ['820e1409162fbd6418b80a0f5a4b50d649ee74f06d195a5210745619b16e1592'], + 'checksums': ['13689f5ec1ab09e8973be81c7f1799b7de4313176072887a9fa0b5825aed3468'], }), ('gam', '1.14-4', { 'checksums': ['6a65d7f707c4833bf2f0b51f959e1bf05d83a75848884b65f6b40787e737aa8e'], diff --git a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb index 9f0f115dfd7..4d6581e3aac 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb @@ -41,6 +41,7 @@ dependencies = [ ('NLopt', '2.4.2'), # for nloptr ('FFTW', '3.3.6'), # for fftw ('libsndfile', '1.0.28'), # for seewave + ('ICU', '61.1'), # for rJava & gdsfmt # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons # ('OpenSSL', '1.0.2h'), @@ -496,7 +497,7 @@ exts_list = [ 'checksums': ['2557d5d59a45620ec9de340c2c25eec4cc478d3fc3f8b87979cf337c5bcfde11'], }), ('foreign', '0.8-69', { - 'checksums': ['820e1409162fbd6418b80a0f5a4b50d649ee74f06d195a5210745619b16e1592'], + 'checksums': ['13689f5ec1ab09e8973be81c7f1799b7de4313176072887a9fa0b5825aed3468'], }), ('gam', '1.14-4', { 'checksums': ['6a65d7f707c4833bf2f0b51f959e1bf05d83a75848884b65f6b40787e737aa8e'], diff --git a/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb new file mode 100644 index 00000000000..5ceadceb99b --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb @@ -0,0 +1,1812 @@ +name = 'R' +version = '3.4.4' +x11ver = '20180131' +versionsuffix = '-X11-%s' % x11ver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2018a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +checksums = ['b3e97d2fab7256d1c655c4075934725ba1cd7cb9237240a11bb22ccdad960337'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('X11', x11ver), + ('Mesa', '17.3.6'), + ('libGLU', '9.0.0'), + ('cairo', '1.14.12'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.3'), + ('zlib', '1.2.11'), + ('SQLite', '3.21.0'), + ('PCRE', '8.41'), + ('libpng', '1.6.34'), # for plotting in R + ('libjpeg-turbo', '1.5.3'), # for plottting in R + ('LibTIFF', '4.0.9'), + ('Java', '1.8.0_162', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.8'), # for tcltk + ('Tk', '8.6.8'), # for tcltk + ('cURL', '7.58.0'), # for RCurl + ('libxml2', '2.9.7'), # for XML + ('GDAL', '2.2.3', '-Python-3.6.4'), # for rgdal + ('PROJ', '5.0.0'), # for rgdal + ('GMP', '6.1.2'), # for igraph + ('NLopt', '2.4.2'), # for nloptr + ('FFTW', '3.3.7'), # for fftw + ('libsndfile', '1.0.28'), # for seewave + ('ICU', '61.1'), # for rJava & gdsfmt + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_default_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on Mar 15 2018 +exts_list = [ + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + ('Rmpi', '0.6-6', { + 'patches': ['Rmpi-0.6-5_impi5.patch'], + 'checksums': [ + 'd8fc09ad38264697caa86079885a7a1098921a3116d5a77a62022b9508f8a63a', # Rmpi_0.6-6.tar.gz + 'f753f0b6434295be70fe29d36edb2047c091e465b7ff0cab56b93d55883c8dd3', # Rmpi-0.6-5_impi5.patch + ], + }), + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.5-8', { + 'checksums': ['7f8bc26e05003168e9d2dadf64eb9a34b51bc41beba482208874803dee7d6c20'], + }), + ('geometry', '0.3-6', { + 'patches': ['geometry-0.3-4-icc.patch'], + 'checksums': [ + '2be231ac99171367635cd957f27da77705329df97520ab86f655839c41dc0968', # geometry_0.3-6.tar.gz + 'df0ea118e597f31561093e01d50698dac3345d40d082eee05360bb4f94378377', # geometry-0.3-4-icc.patch + ], + }), + ('bit', '1.1-12', { + 'checksums': ['ce281c87fb7602bf1a599e72f3e25f9ff7a13e390c124a4506087f69ad79d128'], + }), + ('filehash', '2.4-1', { + 'checksums': ['d0e087d338d89372c251c18fc93b53fb24b1750ea154833216ff16aff3b1eaf4'], + }), + ('ff', '2.2-13', { + 'checksums': ['8bfb08afe0651ef3c23aaad49208146d5f929af5af12a25262fe7743fa346ddb'], + }), + ('bnlearn', '4.3', { + 'checksums': ['78bb1d45977801ffa64f04f4319fa6e1fe9b5268f42b197d33aac074dc46f787'], + }), + ('bootstrap', '2017.2', { + 'checksums': ['44f118c90ee226730175c467a16ac8d5b3169d610424e613da4f73348fd79522'], + }), + ('combinat', '0.0-8', { + 'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'], + }), + ('deal', '1.2-37', { + 'checksums': ['aadfadfd85792b129063d02d5604dbd1afa5aacd2a6ec7eff7458edf2b5dc2da'], + }), + ('fdrtool', '1.2.15', { + 'checksums': ['65f964aa768d0703ceb7a199adc5e79ca79a6d29d7bc053a262eb533697686c0'], + }), + ('formatR', '1.5', { + 'checksums': ['874c197ae3720ec11b44984a055655b99a698e1912104eb9034c11fdf6104da7'], + }), + ('gtools', '3.5.0', { + 'checksums': ['86b6a51a92ddb3c78095e0c5dc20414c67f6e28f915bf0ee11406adad3e476f6'], + }), + ('gdata', '2.18.0', { + 'checksums': ['4b287f59f5bbf5fcbf18db16477852faac4a605b10c5284c46b93fa6e9918d7f'], + }), + ('GSA', '1.03', { + 'checksums': ['dfb84f92508765c74b170bb5bb2b206a11d10fdb4a74473821b0e51cec5d3ac0'], + }), + ('highr', '0.6', { + 'checksums': ['43e152b2dea596df6e14c44398c74fcd438ece15eaae5bdb84aef8d61b213b59'], + }), + ('infotheo', '1.2.0', { + 'checksums': 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}), + ('plogr', '0.1-1', { + 'checksums': ['22755c93c76c26252841f43195df31681ea865e91aa89726010bd1b9288ef48f'], + }), + ('bit64', '0.9-7', { + 'checksums': ['7b9aaa7f971198728c3629f9ba1a1b24d53db5c7e459498b0fdf86bbd3dff61f'], + }), + ('blob', '1.1.0', { + 'checksums': ['16d6603df3ddba177f0ac4d9469c938f89131c4bf8834345db838defd9ffea16'], + }), + ('pkgconfig', '2.0.1', { + 'checksums': ['ab02b2a4b639ba94dcba882a059fe9cddae5498a4309841f764b62ec46ba5a40'], + }), + ('RSQLite', '2.0', { + 'patches': ['RSQLite-2.0-icc.patch'], + 'checksums': [ + '7f0fe629f34641c6af1e8a34412f3089ee2d184853843209d97ffe29430ceff6', # RSQLite_2.0.tar.gz + '828dd9aeb4f8aaff7bccb8671bee757b8001e049ed349d655044e9c916d1860d', # RSQLite-2.0-icc.patch + ], + }), + ('data.table', '1.10.4-3', { + 'checksums': ['ba8b4f1b96b16e7f9765fc49c5028f21ef2210fc46cf962f4f7ea7901f9d8a89'], + }), + ('BatchJobs', '1.7', { + 'checksums': ['49ef69adfb42f085c7ed143a80d78566d55d794ee9a1e1c83d85dbac2a2aa60c'], + }), + ('sandwich', '2.4-0', { + 'checksums': ['34315b9ced76a3ed109aead7b8f77eea6398a6eb2e1ad71515a48bed9808ccc0'], + }), + ('sfsmisc', '1.1-2', { + 'checksums': ['808734644863d102263134634b89dc856dbaadc4d54c32ae697f3e1b0214f831'], + }), + ('spatial', '7.3-11', { + 'checksums': ['624448d2ac22e1798097d09fc5dc4605908a33f490b8ec971fc6ea318a445c11'], + }), + ('VGAM', '1.0-5', { + 'checksums': ['01acf530b011b8f04e1698742c51ea0682d7c9fcdf814fc65ba44869b6e76346'], + }), + ('waveslim', '1.7.5', { + 'checksums': ['31b698f7b19aadcdc02068ee69bf7676cd9dea2913420ce3caa7e507e3a41a53'], + }), + ('xtable', '1.8-2', { + 'checksums': ['1623a1cde2e130fedb46f98840c3a882f1cbb167b292ef2bd86d70baefc4280d'], + }), + ('profileModel', '0.5-9', { + 'checksums': ['c94f25d222521867ddc86021bd0b9a6b9f7b055212985652a8511054b24c2bdd'], + }), + ('brglm', '0.6.1', { + 'checksums': ['b786db50edc703b1b6a986b1ce13d31aab76fd3c672a6540161b25f5cd57239f'], + }), + ('deSolve', '1.20', { + 'checksums': ['56e945835b0c66d36ebc4ec8b55197b616e387d990788a2e52e924ce551ddda2'], + }), + ('tseriesChaos', '0.1-13', { + 'checksums': ['efabf9c59548e2d22aa9763b340789d8e46e88c741ed4a831e52b1ed3bf35038'], + }), + ('tseries', '0.10-43', { + 'checksums': ['c27912f45d6bbd723c8055b345936a3c96ccdc7bd919fad9cf57dc408f845dfa'], + }), + ('fastICA', '1.2-1', { + 'checksums': ['6f2997dd766a544be3a3de2780df48ca67242ac7790a4a2882c417bfaa171f81'], + }), + ('R.methodsS3', '1.7.1', { + 'checksums': ['44b840399266cd27f8f9157777b4d9d85ab7bd31bfdc143b3fc45079a2d8e687'], + }), + ('R.oo', '1.21.0', { + 'checksums': ['645ceec2f815ed39650ca72db87fb4ece7357857875a4ec73e18bfaf647f431c'], + }), + ('cgdsr', '1.2.10', { + 'checksums': ['43bc02fb33c371464f9407d5e5e6419527e9360e3e394343862cca0aebe1d0f7'], + }), + ('R.utils', '2.6.0', { + 'checksums': ['5d64993d1209b512a4e97f2edecdbc185f4a369ee5fa2e334ed2cf017486470e'], + }), + ('R.matlab', '3.6.1', { + 'checksums': ['1032579fd152d419eaf1f69bf6035fba7a71ef26e76136c48a6fc619e3887804'], + }), + ('gbm', '2.1.3', { + 'checksums': ['eaf24be931d762f1ccca4f90e15997719d01005f152160a3d20d858a0bbed92b'], + }), + ('Formula', '1.2-2', { + 'checksums': ['8def4600fb7457d38db8083733477501b54528974aa216e4adf8871bff4aa429'], + }), + ('acepack', '1.4.1', { + 'checksums': ['82750507926f02a696f6cc03693e8d4a5ee7e92500c8c15a16a9c12addcd28b9'], + }), + ('proto', '1.0.0', { + 'checksums': ['9294d9a3b2b680bb6fac17000bfc97453d77c87ef68cfd609b4c4eb6d11d04d1'], + }), + ('gridExtra', '2.3', { + 'checksums': ['81b60ce6f237ec308555471ae0119158b115463df696d2eca9b177ded8988e3b'], + }), + ('chron', '2.3-52', { + 'checksums': ['c47fcf4abb635babe6337604c876d4853d8a24639a98b71523746c56ce75b4a0'], + }), + ('viridis', '0.5.0', { + 'checksums': ['fea477172c1e11be40554545260b36d6ddff3fe6bc3bbed87813ffb77c5546cd'], + }), + ('yaml', '2.1.18', { + 'checksums': ['1bb54d5f28f0adc24a5f3cfbf5cda4a71ca2ad7922a687f756e0619767c1a496'], + }), + ('jsonlite', '1.5', { + 'checksums': ['6490371082a387cb1834048ad8cdecacb8b6b6643751b50298c741490c798e02'], + }), + ('htmltools', '0.3.6', { + 'checksums': ['44affb82f9c2fd76c9e2b58f9229adb003217932b68c3fdbf1327c8d74c868a2'], + }), + ('htmlwidgets', '1.0', { + 'checksums': ['9973fe7a0271d1f39317fad58edee818eae8df26d037f0341024d032e0af9326'], + }), + ('knitr', '1.20', { + 'checksums': ['7b2409056af001970d1ed502a25fd84536aca4a21039479998507556446d0890'], + }), + ('rstudioapi', '0.7', { + 'checksums': ['a541bc76ef082d2c27e42fd683f8262cb195b1497af3509178d2642870397a8c'], + }), + ('bindr', '0.1.1', { + 'checksums': ['7c785ca77ceb3ab9282148bcecf64d1857d35f5b800531d49483622fe67505d0'], + }), + ('bindrcpp', '0.2', { + 'checksums': ['d0efa1313cb8148880f7902a4267de1dcedae916f28d9a0ef5911f44bf103450'], + }), + ('dplyr', '0.7.4', { + 'checksums': ['7b1fc90750fbb46483423da6721832c545d37b157f4f3355784a65e50fada8c2'], + }), + ('purrr', '0.2.4', { + 'checksums': ['ed8d0f69d29b95c2289ae52be08a0e65f8171abb6d2587de7b57328bf3b2eb71'], + }), + ('tidyselect', '0.2.4', { + 'checksums': ['5cb30e56ad5c1ac59786969edc8d542a7a1735a129a474f585a141aefe6a2295'], + }), + ('tidyr', '0.8.0', { + 'checksums': ['0b7fb3e4ee7c6c8bb9894825c7f16db967abb57aceac0609b7866fa1825c57e2'], + }), + ('htmlTable', '1.11.2', { + 'checksums': ['64a273b1cdf07a7c57b9031315ca665f95d78e70b4320d020f64a139278877d1'], + }), + ('Hmisc', '4.1-1', { + 'checksums': ['991db21cdf73ffbf5b0239a4876b2e76fd243ea33528afd88dc968792f281498'], + }), + ('fastcluster', '1.1.24', { + 'checksums': ['82c939b79dbaf00c79b01f19b09a8fadb9a949397b8f65bc861c552e0485b995'], + }), + ('registry', '0.5', { + 'checksums': ['5d8be59ba791987b2400e9e8eaaac614cd544c1aece785ec4782ea6d5ea00efb'], + }), + ('pkgmaker', '0.22', { + 'checksums': ['19ad78c16bd5757333e7abbd5eebcec081deb494c9a4b6eec6919a3747b3386f'], + }), + ('rngtools', '1.2.4', { + 'checksums': ['27019835b750f470b13dbb7fecd3b839a61b52774e23fffa191f919533768fb9'], + }), + ('doParallel', '1.0.11', { + 'checksums': ['4ccbd2eb46d3e4f5251b0c3de4d93d9168b02bb0be493656d6aea236667ff76a'], + }), + ('gridBase', '0.4-7', { + 'checksums': ['be8718d24cd10f6e323dce91b15fc40ed88bccaa26acf3192d5e38fe33e15f26'], + }), + ('NMF', '0.21.0', { + 'checksums': ['3b30c81c66066fab4a63c5611a0313418b840d8b63414db31ef0e932872d02e3'], + }), + ('irlba', '2.3.2', { + 'checksums': ['3fdf2d8fefa6ab14cd0992740de7958f9f501c71aca93229f5eb03c54558fc38'], + }), + ('igraph', '1.2.1', { + 'checksums': ['55341848f85a436c32d60f59a4db485238d535f2e8afe0d5a360804fc33299c1'], + }), + ('GeneNet', '1.2.13', { + 'checksums': ['3798caac3bef7dc87f97b3628eb29eb12365d571ce0837b5b6285b0be655a270'], + }), + ('ape', '5.0', { + 'checksums': ['c32ed22e350b3d7c7ef3de9334155ab1f3086922b5ec9a1643897cae7abda960'], + }), + ('RJSONIO', '1.3-0', { + 'checksums': ['119334b7761c6c1c3cec52fa17dbc1b72eaebb520c53e68d873dea147cf48fb7'], + }), + ('caTools', '1.17.1', { + 'checksums': ['d32a73febf00930355cc00f3e4e71357412e0f163faae6a4bf7f552cacfe9af4'], + }), + ('gplots', '3.0.1', { + 'checksums': ['343df84327ac3d03494992e79ee3afc78ba3bdc08af9a305ee3fb0a38745cb0a'], + }), + ('ROCR', '1.0-7', { + 'checksums': ['e7ef710f847e441a48b20fdc781dbc1377f5a060a5ee635234053f7a2a435ec9'], + }), + ('httpuv', '1.3.6.2', { + 'checksums': ['8e8ca2f15529089846695abdab229cbc9812f0b2710855fb0a41ac720a9f7040'], + }), + ('rjson', '0.2.15', { + 'checksums': ['77d00d8f6a1c936329b46f3b8b0be79a165f8c5f1989497f942ecc53dcf6f2ef'], + }), + ('sourcetools', '0.1.6', { + 'checksums': ['c9f48d2f0b7f7ed0e7fecdf8e730b0b80c4d567f0e1e880d118b0944b1330c51'], + }), + ('shiny', '1.0.5', { + 'checksums': ['20e25f3f72f3608a2151663f7836f2e0c6da32683a555d7541063ae7a935fa42'], + }), + ('seqinr', '3.4-5', { + 'checksums': ['162a347495fd52cbb62e8187a4692e7c50b9fa62123c5ef98f2744c98a05fb9f'], + }), + ('LearnBayes', '2.15', { + 'checksums': ['45c91114b4aaa0314feeb4311dbe78f5b75a3b76bb2d1ca0f8adb2e0f1cbe233'], + }), + ('deldir', '0.1-14', { + 'checksums': ['89d365a980ef8589971e5d311c6bd59fe32c48dbac8000a880b9655032c99289'], + }), + ('gmodels', '2.16.2', { + 'checksums': ['ab018894bdb376c5bd6bc4fbc4fe6e86590f4106795a586ef196fbb6699ec47d'], + }), + ('expm', '0.999-2', { + 'checksums': ['38f1e5bfa90f794486789695d0d9e49158c7eb9445dc171dd83dec3d8fa130d6'], + }), + ('spData', '0.2.8.1', { + 'checksums': ['64e389474bd45f39b2cdf4ba8e5bf872a6f52cbf83deca10111df1000e7b7951'], + }), + ('spdep', '0.7-4', { + 'checksums': ['9643f1e509e0107c8f8d949b0a6cbb6a274c7ca1e9ba4d474ce42235696653c7'], + }), + ('vegan', '2.4-6', { + 'checksums': ['dc9c1b0832835e1dd9e0ed3d9066e0834f4b15f2330f771f4abed72a48c6b59c'], + }), + ('adegenet', '2.1.1', { + 'checksums': ['3043fe5d731a38ff0e266f090dcda448640c3d0fd61934c76da32d082e5dce7a'], + }), + ('prettyunits', '1.0.2', { + 'checksums': ['35a4980586c20650538ae1e4fed4d80fdde3f212b98546fc3c7d9469a1207f5c'], + }), + ('progress', '1.1.2', { + 'checksums': ['a9f4abfd9579b80967cd681041643fe9dfcc4eb3beeba45391bb64e9209baabb'], + }), + ('rncl', '0.8.2', { + 'checksums': ['80e1aa00cab4af0093198d0d902c973eb31dbdf4628e229ee9c136a9cc9c369e'], + }), + ('XML', '3.98-1.10', { + 'checksums': ['a19e04178e420c0cbf8a2d55513ea568c7c13aa53a6c1f1c3de652ba56525fb9'], + }), + ('praise', '1.0.0', { + 'checksums': ['5c035e74fd05dfa59b03afe0d5f4c53fbf34144e175e90c53d09c6baedf5debd'], + }), + ('withr', '2.1.1', { + 'checksums': ['bd5fae3846b8f89081a0991375402266dccf49bfa5d614690deea1b03ba5eb9e'], + }), + ('testthat', '2.0.0', { + 'checksums': ['3bc047ad1c4522104023d4fbbfc9aceed14d316fdb16865a514f26b3e628b494'], + }), + ('rprojroot', '1.3-2', { + 'checksums': ['df5665834941d8b0e377a8810a04f98552201678300f168de5f58a587b73238b'], + }), + ('rmarkdown', '1.9', { + 'checksums': ['cbb7da80b514c148b48b8d4b6d497ec8edf6d2f6be3c483c836eec99e19a0673'], + }), + ('openssl', '1.0.1', { + 'checksums': 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('rredlist', '0.4.0', { + 'checksums': ['9e59d3c5830322ed85762bbb3273b59befe59c3feabfe7d2f32de96fc4525048'], + }), + ('rentrez', '1.2.1', { + 'checksums': ['74cf6dbe1b229518c25221534b20437b53cb663f1473cf9df5a59ca76b76ae84'], + }), + ('rotl', '3.0.3', { + 'checksums': ['049a417ee10203339b3543fd97116b59de467344493f234d0d01c4b6ad7fd75d'], + }), + ('solrium', '1.0.0', { + 'checksums': ['0e362d4f3b700997bc417ea3ca21301ddbd7978ab3394affbe6861eb27308ee6'], + }), + ('ritis', '0.7.0', { + 'checksums': ['bb3a3243f83083e7dd874624e8dfb57953c8aea38df16b3e5c0163857e875d38'], + }), + ('worrms', '0.2.0', { + 'checksums': ['66f6238988b3deeecc1dee628979727c98b3db072b046e316ff8962192141bd7'], + }), + ('natserv', '0.1.4', { + 'checksums': ['07501608a2e79b20940cd0e22aca9db6150942eed5b6dad184ec957e153d8e63'], + }), + ('WikipediR', '1.5.0', { + 'checksums': ['f8d0e6f04fb65f7ad9c1c068852a6a8b699ffe8d39edf1f3fa07d32d087e8ff0'], + }), + ('WikidataR', '1.4.0', { + 'checksums': ['64b1d53d7023249b73a77a7146adc3a8957b7bf3d808ebd6734795e9f58f4b2a'], + }), + ('wikitaxa', '0.2.0', { + 'checksums': ['944523717b2571af02a6bf15a58100dfb69530f702ab919f1c5fd3d263588c19'], + }), + ('taxize', '0.9.2', { + 'checksums': ['15aacbdd61a77b27a6faa8e0c6fd05b2e96cba51eb94cefd623f29428c4cbb97'], + }), + ('uuid', '0.1-2', { + 'checksums': ['dd71704dc336b0857981b92a75ed9877d4ca47780b1682def28839304cd3b1be'], + }), + ('RNeXML', '2.0.8', { + 'checksums': ['b2bc118a3982866d12aa880823a17e0247915a0fa265163a383bc26981d96d46'], + }), + ('phylobase', '0.8.4', { + 'checksums': ['d7c1a972c266ffe80345c7150608a85e6e2def4a3f079ac964ad9dbce2281002'], + }), + ('adephylo', '1.1-11', { + 'checksums': ['154bf2645eac4493b85877933b9445442524ca4891aefe4e80c294c398cff61a'], + }), + ('animation', '2.5', { + 'checksums': ['b232fef1b318c79710e5e1923d87baba4c85ffe2c77ddb188130e0911d8cb55f'], + }), + ('bigmemory.sri', '0.1.3', { + 'checksums': ['55403252d8bae9627476d1f553236ea5dc7aa6e54da6980526a6cdc66924e155'], + }), + ('bigmemory', '4.5.33', { + 'checksums': [ + '7237d9785d8ce3eab4e36ad3ce2c95cbae926326031661b4f237b7517f4b9479', # bigmemory_4.5.33.tar.gz + ], + }), + ('calibrate', '1.7.2', { + 'checksums': ['78066a564f57f2110f1752d681d6b97915cf73135134330587fff8b46c581604'], + }), + ('clusterGeneration', '1.3.4', { + 'checksums': ['7c591ad95a8a9d7fb0e4d5d80dfd78f7d6a63cf7d11eb53dd3c98fdfb5b868aa'], + }), + ('raster', '2.6-7', { + 'checksums': ['fb91804fd465a4a6d9d9858e29fd05f41a99b8efdcc5cf4370ea253b68e42b01'], + }), + ('dismo', '1.1-4', { + 'checksums': ['f2110f716cd9e4cca5fd2b22130c6954658aaf61361d2fe688ba22bbfdfa97c8'], + }), + ('extrafontdb', '1.0', { + 'checksums': ['faa1bafee5d4fbc24d03ed237f29f1179964ebac6e3a46ac25b0eceda020b684'], + }), + ('Rttf2pt1', '1.3.6', { + 'checksums': ['4eb1f3e0e5bcb11f8e2f6fa7d5ecb3410287291ba538f615872ab78fac20f1a2'], + }), + ('extrafont', '0.17', { + 'checksums': ['2f6d7d79a890424b56ddbdced361f8b9ddede5edd33e090b816b88a99315332d'], + }), + ('fields', '9.6', { + 'checksums': ['410424d74861ad0ba16f26e2b44bd63a9b590a190cc98c048dac55891422ffec'], + }), + ('shapefiles', '0.7', { + 'checksums': ['eeb18ea4165119519a978d4a2ba1ecbb47649deb96a7f617f5b3100d63b3f021'], + }), + ('fossil', '0.3.7', { + 'checksums': ['3feba6ceecaa6f2f68fdc1ceb0019395ccfadb0cf033e1709dddb690c7f210a1'], + }), + ('geiger', '2.0.6', { + 'checksums': ['e13b2c526378eaf9356b00bbe21b3c2c956327f8062fed638ccc1f49591c3eff'], + }), + ('glmnet', '2.0-13', { + 'checksums': ['f3288dcaddb2f7014d42b755bede6563f73c17bc87f8292c2ef7776cb9b9b8fd'], + }), + ('crosstalk', '1.0.0', { + 'checksums': ['b31eada24cac26f24c9763d9a8cbe0adfd87b264cf57f8725027fe0c7742ca51'], + }), + ('rgl', '0.99.9', { + 'checksums': ['b5bdc24ba7f86b940158ad72ac9069e7b80067f103493fc916a6af3a007e64e7'], + }), + ('labdsv', '1.8-0', { + 'checksums': ['dfaeb03a6e1bab6cfd384c00671235b22f2b4254cac1129b24a348cb353b6e65'], + }), + ('stabs', '0.6-3', { + 'checksums': ['e961ae21d45babc1162b6eeda874c4e3677fc286fd06f5427f071ad7a5064a9f'], + }), + ('modeltools', '0.2-21', { + 'checksums': ['07b331475625674ab00e6ddfc479cbdbf0b22d5d237e8c25d83ddf3e0ad1cd7a'], + }), + ('strucchange', '1.5-1', { + 'checksums': ['740e2e20477b9fceeef767ae1002adc5ec397cb0f7daba5289a2c23b0dddaf31'], + }), + ('TH.data', '1.0-8', { + 'checksums': ['478f109fcc1226500ead8e3bd6e047cecde2294fde4df8ec216d38313db79a9d'], + }), + ('multcomp', '1.4-8', { + 'checksums': ['a20876619312310e9523d67e9090af501383ce49dc6113c6b4ca30f9c943a73a'], + }), + ('coin', '1.2-2', { + 'checksums': ['d518065d3e1eb00121cb4e0200e1e4ae6b68eca6e249afc38bbffa35d24105bb'], + }), + ('party', '1.2-4', { + 'checksums': ['6c1d3ee9ce6f1ce8e33eefc3d28a504406be6470cac4da6dd4aab09166ff2182'], + }), + ('mboost', '2.8-1', { + 'checksums': ['96a8b7daf5c6bc9240ad2e398867834ec18918c6cbdf64804ddc100a9b717798'], + }), + ('msm', '1.6.6', { + 'checksums': ['fd12512d3cdca5fab634bf6222d896482bd1876192939da475f251b3a873a71a'], + }), + ('nor1mix', '1.2-3', { + 'checksums': ['435e6519e832ef5229c51ccb2619640e6b50dfc7470f70f0c938d18a114273af'], + }), + ('np', '0.60-6', { + 'checksums': ['59c37424161cfac331d1c8b6feec747010445f18f3c72e3c7bac269964e9e2f8'], + }), + ('polynom', '1.3-9', { + 'checksums': ['d35a50925cc5552a6aac0816a91dbc03e9fd77da47e06d27572fde9dcbee9de8'], + }), + ('polspline', '1.1.12', { + 'checksums': ['fc6bd2e0cca8c13cf099c54fe1e740730e26bb9793d439c395cf16ec8c2b0f32'], + }), + ('rms', '5.1-2', { + 'checksums': ['f1cfeef466ac436105756679353a3468027d97a600e3be755b819aef30ed9207'], + }), + ('RWekajars', '3.9.2-1', { + 'checksums': ['0e6c00ea2a0798dec828a3a3eb61fbcf43da305f1664f62774fbdb8e473dd600'], + }), + ('RWeka', '0.4-37', { + 'checksums': ['fc0a3bb09b9d4dfefd7c3ada038d5d6b03c5091e1206e88ef7f045c18f8f19e0'], + }), + ('slam', '0.1-42', { + 'checksums': ['7206b0189544c9878b83005f80f89626cc2c53cfe3e640aeaa9c3da1f07675df'], + }), + ('tm', '0.7-3', { + 'checksums': ['f3c3e151e621ffb0c82048b5bf9c2a34c8fb34cf5d2943544979b4fcc2cc1c11'], + }), + ('TraMineR', '2.0-8', { + 'checksums': ['394d4481707dfd8a4b0e28681097948ab36934dbe4084cf0917ae5f3e0bb9774'], + }), + ('chemometrics', '1.4.2', { + 'checksums': ['b705832fa167dc24b52b642f571ed1efd24c5f53ba60d02c7797986481b6186a'], + }), + ('FNN', '1.1', { + 'checksums': ['b2a2e97af14aa50ef4dce15a170e1d7329aebb7643bab4a6cf35609555acccce'], + }), + ('ipred', '0.9-6', { + 'checksums': ['b8d36438eb9b7209d27b85738dcad03b2e535dcb2f4191432780d9cbf00d3cef'], + }), + ('statmod', '1.4.30', { + 'checksums': ['9d2c1722a85f53623a9ee9f73d835119ae22ae2b8ec7b50d675401e314ea641f'], + }), + ('miscTools', '0.6-22', { + 'checksums': ['d00bb2602d1d31e9e1e13c8868cfe69d432bbe15afa8d4bbb83b3c9e0b9dcfea'], + }), + ('maxLik', '1.3-4', { + 'checksums': ['181ab87721b1e6e3859c60d12eea2f67a7135bfa679db73c20a9ef76d82c4b4a'], + }), + ('mlogit', '0.2-4', { + 'checksums': ['5d9f5d20efd9d654e15875d813d9da3e756c7b8f25d8bb1f5d689a128fa7cd96'], + }), + ('getopt', '1.20.2', { + 'checksums': ['3d6c12d32d6cd4b2909be626e570e158b3ed960e4739510e3a251e7f172de38e'], + }), + ('gsalib', '2.1', { + 'checksums': ['e1b23b986c18b89a94c58d9db45e552d1bce484300461803740dacdf7c937fcc'], + }), + ('optparse', '1.4.4', { + 'checksums': ['0b1f1d336f1be386260fb5bbdf74f01787c09176d69febf8d563e5af75e5c4b9'], + }), + ('miniUI', '0.1.1', { + 'checksums': ['9c92032071ee75ee9c26c4cfd3115877fbcb15de2fd2023109c670784b51cce1'], + }), + ('hms', '0.4.2', { + 'checksums': ['a57820b3e3221e973cba9500b4ad7953730110ee398693d150af833f26d5d0bc'], + }), + ('readr', '1.1.1', { + 'checksums': ['1a29b99009a06f2cee18d08bc6201fd4985b6d45c76cefca65084dcc1a2f7cb3'], + }), + ('forcats', '0.3.0', { + 'checksums': ['95814610ec18b8a8830eba63751954387f9d21400d6ab40394ed0ff22c0cb657'], + }), + ('haven', '1.1.1', { + 'checksums': ['5f7bf6dbee431b4e64771d9d97ee2c3da5b8f66a5e81fd1ec78a236eb3de6cba'], + }), + ('labelled', '1.0.1', { + 'checksums': ['9b7f1c5644f0e30496c291c84c52204b47d2b7da9aaefa332898aaae3226bfa2'], + }), + ('classInt', '0.1-24', { + 'checksums': ['f3dc9084450ea3da07e1ea5eeb097fd2fedc7e29e5d7794b418bcb438c4fcfa2'], + }), + ('questionr', '0.6.2', { + 'checksums': ['1dcad3c980548352f3a775ec089359b3f7737762e97c2a97c9a39cda4de54f56'], + }), + ('klaR', '0.6-13', { + 'checksums': ['56b9689fc7ed5ece159056bcea181c9e670205a570095e76779a2a03d156171b'], + }), + ('neuRosim', '0.2-12', { + 'checksums': ['f4f718c7bea2f4b61a914023015f4c71312f8a180124dcbc2327b71b7be256c3'], + }), + ('locfit', '1.5-9.1', { + 'checksums': ['f524148fdb29aac3a178618f88718d3d4ac91283014091aa11a01f1c70cd4e51'], + }), + ('GGally', '1.3.2', { + 'checksums': ['f4143f45254fed794be991180aeffe459f6756bfa08acad963707d8e843cfd0a'], + }), + ('beanplot', '1.2', { + 'checksums': ['49da299139a47171c5b4ccdea79ffbbc152894e05d552e676f135147c0c9b372'], + }), + ('clValid', '0.6-6', { + 'checksums': ['c13ef1b6258e34ba53615b78f39dbe4d8ba47b976b3c24a3eedaecf5ffba19ed'], + }), + ('matrixStats', '0.53.1', { + 'checksums': ['df70bc9fb64716a7a633b5d0c2a2422b2c8d93ac5e64574528a325505df9712e'], + }), + ('DiscriMiner', '0.1-29', { + 'checksums': ['5aab7671086ef9940e030324651976456f0e84dab35edb7048693ade885228c6'], + }), + ('ellipse', '0.4.1', { + 'checksums': ['1a9a9c52195b26c2b4d51ad159ab98aff7aa8ca25fdc6b2198818d1a0adb023d'], + }), + ('leaps', '3.0', { + 'checksums': ['55a879cdad5a4c9bc3b5697dd4d364b3a094a49d8facb6692f5ce6af82adf285'], + }), + ('nloptr', '1.0.4', { + 'checksums': ['84225b993cb1ef7854edda9629858662cc8592b0d1344baadea4177486ece1eb'], + }), + ('lme4', '1.1-15', { + 'checksums': ['7d9fd6309aae9cfa691236b3841a60f88ec70110faf2c1dabcbdff18e1ce8669'], + }), + ('pbkrtest', '0.4-7', { + 'checksums': ['5cbb03ad2b2468720a5a610a0ebda48ac08119a34fca77810a85f554225c23ea'], + }), + ('car', '2.1-6', { + 'checksums': ['d2426a66f63324d9db34dc89becb728d2d4b6d5f183f2efe02cbf683646a8492'], + }), + ('flashClust', '1.01-2', { + 'checksums': ['48a7849bb86530465ff3fbfac1c273f0df4b846e67d5eee87187d250c8bf9450'], + }), + ('FactoMineR', '1.39', { + 'checksums': ['b0bb1d6d7d1f3cb11a4b63c377321e10078a36f29bc78dfa3b80c7c149f4a08a'], + }), + ('flexclust', '1.3-5', { + 'checksums': ['dbf49969c93a7b314d9dc3299a0764ed9a804ba7dcbdc08a1235f244f4b85059'], + }), + ('flexmix', '2.3-14', { + 'checksums': ['837c7f175a211b3c484b2c7b81ec9729889a614c5c6e7d70c95a2c1d60ff846a'], + }), + ('prabclus', '2.2-6', { + 'checksums': ['41792980e40ba18204fab92d85120dcd468860e2204e52fb42636c6f7aee5a62'], + }), + ('diptest', '0.75-7', { + 'checksums': ['462900100ca598ef21dbe566bf1ab2ce7c49cdeab6b7a600a50489b05f61b61b'], + }), + ('trimcluster', '0.1-2', { + 'checksums': ['622fb61580cc19b9061c6ee28ffd751250a127f07904b45a0e1c5438d25b4f53'], + }), + ('fpc', '2.1-11', { + 'checksums': ['5975b31b63ad1e7b9c081ae42414e3d4de7a45e1a80100c2931aae5716d65411'], + }), + ('BiasedUrn', '1.07', { + 'checksums': ['2377c2e59d68e758a566452d7e07e88663ae61a182b9ee455d8b4269dda3228e'], + }), + ('TeachingDemos', '2.10', { + 'checksums': ['2ef4c2e36ba13e32f66000e84281a3616584c86b255bca8643ff3fe4f78ed704'], + }), + ('kohonen', '3.0.4', { + 'checksums': [ + '429864d72858c29d4187bed48ac1c17cf2ecb08f18090b6bf44dff55174609ab', # kohonen_3.0.4.tar.gz + ], + }), + ('base64', '2.0', { + 'checksums': ['8e259c2b12446197d1152b83a81bab84ccb5a5b77021a9b5645dd4c63c804bd1'], + }), + ('doRNG', '1.6.6', { + 'checksums': ['939c2282c72c0b89fc7510f4bff901a4e99007dc006f46762c8f594c0ecbd876'], + }), + ('nleqslv', '3.3.1', { + 'checksums': ['87eee7dad496539ede21bdb02bb0bc3793c9a390c000b0cd2bcd9b41ce5d3ad8'], + }), + ('Deriv', '3.8.4', { + 'checksums': ['de4b7dfd4653dec9ae49987b8588c5ecfd7ef59081d9a1c55834da94bb5342d1'], + }), + ('RGCCA', '2.1.2', { + 'checksums': ['20f341fca8f616c556699790814debdf2ac7aa4dd9ace2071100c66af1549d7d'], + }), + ('pheatmap', '1.0.8', { + 'checksums': ['51468765380119c302ee9afd52d0483123c0670297f4b906edc79235939960c6'], + }), + ('openxlsx', '4.0.17', { + 'checksums': ['116b9829c5a85ab1b7368d9f7f34a2248436f54bbf6ad635186c8a70b5a204d7'], + }), + ('pvclust', '2.0-0', { + 'checksums': ['1a4615214992307fd7c786cf4607a3ae2af5c0d4067f5053e1c195798a70d741'], + }), + ('RCircos', '1.2.0', { + 'checksums': ['7fd06e2efc33b5c30fc4ba3945b04021f255ba4ffcc394348df7488b9394444a'], + }), + ('lambda.r', '1.2', { + 'checksums': ['7dc4188ce1d4a6b026a1b128719ff60234ae1e3ffa583941bbcd8473ad18146f'], + }), + ('futile.options', '1.0.0', { + 'checksums': ['ee84ece359397fbb63f145d11af678f5c8618570971e78cc64ac60dc0d14e8c2'], + }), + ('futile.logger', '1.4.3', { + 'checksums': ['5e8b32d65f77a86d17d90fd8690fc085aa0612df8018e4d6d6c1a60fa65776e4'], + }), + ('VennDiagram', '1.6.19', { + 'checksums': ['c2baf466e072878643a28e971f11691dc830610ae8e7077d1adbd0be73e11338'], + }), + ('xlsxjars', '0.6.1', { + 'checksums': ['37c1517f95f8bca6e3514429394d2457b9e62383305eba288416fb53ab2e6ae6'], + }), + ('xlsx', '0.5.7', { + 'checksums': ['36727bc330c281dab8a028fab2dde92d032345974b15e3dde920ee16dc6db363'], + }), + ('forecast', '8.2', { + 'checksums': [ + 'eb3fab64ed139d068e7d026cd3880f1b623f4153a832fb71845488fa75e8b812', # forecast_8.2.tar.gz + ], + }), + ('fma', '2.3', { + 'checksums': ['f516eff79e14d4ffefcdc2db06d97ae57f998e37e871264457078f671384fafc'], + }), + ('expsmooth', '2.3', { + 'checksums': ['ac7da36347f983d6ec71715daefd2797fe2fc505c019f4965cff9f77ce79982a'], + }), + ('fpp', '0.5', { + 'checksums': ['9c87dd8591b8a87327cae7a03fd362a5492495a96609e5845ccbeefb96e916cb'], + }), + ('maptools', '0.9-2', { + 'checksums': ['3bf88cd06f69168d169727ca90d378dfedca77d80ebd26380b2708b3c6aab41c'], + }), + ('tensor', '1.5', { + 'checksums': ['e1dec23e3913a82e2c79e76313911db9050fb82711a0da227f94fc6df2d3aea6'], + }), + ('polyclip', '1.6-1', { + 'checksums': ['c33aac743f1a4c35d37791486a6628838f5fbff51001b4270aba813163e1bd1f'], + }), + ('goftest', '1.1-1', { + 'checksums': ['db6cb1ff6e18520b172e93fca5d7d953bd2d06f4af73bf90aa0a09df8cad71a0'], + }), + ('spatstat.utils', '1.8-0', { + 'checksums': ['cf412cb4ef44af63e8c9e01ca2aa86d665788cdb128fba5a0d9c499beb317214'], + }), + ('spatstat.data', '1.2-0', { + 'checksums': ['f5f1da10a19b1eb3911d56aadea294e1c428d332076cf2ca8ad50c1b832ffc5b'], + }), + ('spatstat', '1.55-0', { + 'checksums': ['6392b947a2c970dc3d1787d077398c67e0b8ab053061e4d8a4ad12de3ee0b716'], + }), + ('rgdal', '1.2-16', { + 'checksums': ['017fefea4f9a6d4540d128c707197b7025b55e4aff98fc763065366b025b03c9'], + }), + ('gdalUtils', '2.0.1.7', { + 'checksums': ['931138a03b37678f47a41a27dca4ba1938bed07a8a3e869f42feaa76aa380c59'], + }), + ('pracma', '2.1.4', { + 'checksums': ['0ccaef86c1446971ca244e6dbcc605222c2f652b23a5db921070e37a6240f5f9'], + }), + ('RCurl', '1.95-4.10', { + 'checksums': ['6f8324f1cb2de6ca818851bd9b83be33083f8752e76ce4187b7c39bda781fe0a'], + }), + ('bio3d', '2.3-3', { + 'checksums': ['f4b45847eb8a4175dacea659f30a8075769ec1ae19daec6842b0d72227b48633'], + }), + ('AUC', '0.3.0', { + 'checksums': ['e705f2c63d336249d19187f3401120d738d42d323fce905f3e157c2c56643766'], + }), + ('interpretR', '0.2.4', { + 'checksums': ['4c08a6dffd6fd5764f27812f3a085c53e6a21d59ae82d903c9c0da93fd1dd059'], + }), + ('cvAUC', '1.1.0', { + 'checksums': ['c4d8ed53b93869650aa2f666cf6d1076980cbfea7fa41f0b8227595be849738d'], + }), + ('SuperLearner', '2.0-23', { + 'checksums': ['846c01080256d4c1d4570535599662ee8bcd95ceff753f2bcaaff0cf5a7f7a11'], + }), + ('lpSolve', '5.6.13', { + 'checksums': ['d5d41c53212dead4fd8e6425a9d3c5767cdc5feb19d768a4704116d791cf498d'], + }), + ('mediation', '4.4.6', { + 'checksums': ['b17784c001305d5f3b84573a673cef31475520d9baec972e42431be193bf305f'], + }), + ('ModelMetrics', '1.1.0', { + 'checksums': ['487d53fda57da4b29f83a927dda8b1ae6655ab044ee3eec33c38aeb27eed3d85'], + }), + ('CVST', '0.2-1', { + 'checksums': ['a27fd2bfa778fce9b9a68d2b9206c66af27b3c36a973dd45ce673886a267aa9f'], + }), + ('DRR', '0.0.3', { + 'checksums': ['7493389c1fb9ddc4d4261e15bf2d4198603227275688b1d3e3994d47e976a1f9'], + }), + ('dimRed', '0.1.0', { + 'checksums': ['fb0cef7a21b8a5219c74e5227a282168599dd63e904130366f3d2fed8a625a39'], + }), + ('lubridate', '1.7.3', { + 'checksums': ['2cffbf54afce1d068e65241fb876a77b10ee907d5a19d2ffa84d5ba8a2c3f3df'], + }), + ('ddalpha', '1.3.1.1', { + 'checksums': ['fe70c65758fc75365ac6ee537010777b24cb49fb830c5c899a19a0964b8e888f'], + }), + ('gower', '0.1.2', { + 'checksums': ['eb91b2d2784d237c7055abcf3cfa4fc0b2226b855a0c29fc5a4e8eaa689079d5'], + }), + ('RcppRoll', '0.2.2', { + 'checksums': ['51c76812687e2a8572c6037b0c095c0a30ee6a24783edf2c7c717d547ddfbfa7'], + }), + ('psych', '1.7.8', { + 'checksums': ['f328ea602e22b0e7e5f310a8d19f305d8e0a3a86040cdfb64863b68b56d55135'], + }), + ('broom', '0.4.3', { + 'checksums': ['2e261b40006432e787dc208c2a8943c6ae714968879dd3361ba1ee6ea5603785'], + }), + ('recipes', '0.1.2', { + 'checksums': ['891a30cce1529e29a832f3aab92b38c9a0ef959a6fb144c0bf07595c871a59b1'], + }), + ('caret', '6.0-78', { + 'checksums': ['dea8799853b9b0843d994b4dad09d1535547f36752ff70a956004111e3ef3640'], + }), + ('adabag', '4.2', { + 'checksums': ['47019eb8cefc8372996fbb2642f64d4a91d7cedc192690a8d8be6e7e03cd3c81'], + }), + ('parallelMap', '1.3', { + 'checksums': ['a52d93572c1b85281e41d8e3c2db97dda5fce96c222e04171b4489ec5000cd08'], + }), + ('ParamHelpers', '1.10', { + 'checksums': ['80629ba62e93b0b706bf2e451578b94fbb9c5b95ff109ecfb5b011bfe0a0fa5b'], + }), + ('ggvis', '0.4.3', { + 'checksums': ['34d517783016aaa1c4bef8972f4c06df5cd9ca0568035b647e60a8369043ecdc'], + }), + ('mlr', '2.12', { + 'checksums': ['cfe00089ae4cd88c6d03826eda43d4fe29e467e3a7c95d103fafca8308f5c161'], + }), + ('unbalanced', '2.0', { + 'checksums': ['9be32b1ce9d972f1abfff2fbe18f5bb5ba9c3f4fb1282063dc410b82ad4d1ea2'], + }), + ('RSNNS', '0.4-10', { + 'checksums': ['f00d34a62e67ec14a7c1963f9f7f0f01c94fcf79ec7a5774a2fa49e475d81ace'], + }), + ('abc.data', '1.0', { + 'checksums': ['b242f43c3d05de2e8962d25181c6b1bb6ca1852d4838868ae6241ca890b161af'], + }), + ('abc', '2.1', { + 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], + }), + ('lhs', '0.16', { + 'checksums': ['9cd199c3b5b2be1736d585ef0fd39a00e31fc015a053333a7a319668d0809425'], + }), + ('tensorA', '0.36', { + 'checksums': ['97b3e72f26ca3a756d045008764d787a32c68f0a276fb7a29b6e1b4592fdecf6'], + }), + ('EasyABC', '1.5', { + 'checksums': ['1dd7b1383a7c891cafb34d9cec65d92f1511a336cff1b219e63c0aa791371b9f'], + }), + ('shape', '1.4.4', { + 'checksums': ['f4cb1b7d7c84cf08d2fa97f712ea7eb53ed5fa16e5c7293b820bceabea984d41'], + }), + ('whisker', '0.3-2', { + 'checksums': ['484836510fcf123a66ddd13cdc8f32eb98e814cad82ed30c0294f55742b08c7c'], + }), + ('commonmark', '1.4', { + 'checksums': ['865ecf9432763393ca9de52d0106a58c4be9e8d5196da60e068eed0b67ca68ed'], + }), + ('desc', '1.1.1', { + 'checksums': ['32ff99b658db3bf0172cf30d15b7f34021144ffc08a5896afd3d30055fc4074c'], + }), + ('roxygen2', '6.0.1', { + 'checksums': ['d22ddc05cd5308a48b8359b932e1f7f4c23fdf0c857ac8e52c42381b6bfcff76'], + }), + ('git2r', '0.21.0', { + 'checksums': ['0480e4c47394ad1724c80982eff3be5ce34168046939340bf22cc1df6b6baf87'], + }), + ('rversions', '1.0.3', { + 'checksums': ['21d0809f46505de89a2be7be9449e39c39cff5bc77e584dec976ee6c0b884f44'], + }), + ('devtools', '1.13.5', { + 'checksums': ['fa59488415d7b601dc743cf6080834e6fbd49dda6ecd60629cca0fd8ced47cf4'], + }), + ('Rook', '1.1-1', { + 'checksums': ['00f4ecfa4c5c57018acbb749080c07154549a6ecaa8d4130dd9de79427504903'], + }), + ('Cairo', '1.5-9', { + 'patches': ['Cairo-1.5-9.patch'], + 'checksums': [ + '2a867b6cae96671d6bc3acf9334d6615dc01f6ecf1953a27cde8a43c724a38f4', # Cairo_1.5-9.tar.gz + '3efa99888503949eefe586faf3f6f80566674c5a8cfb2c62b648b42f22466dfa', # Cairo-1.5-9.patch + ], + }), + ('RMTstat', '0.3', { + 'checksums': ['81eb4c5434d04cb66c749a434c33ceb1c07d92ba79765d4e9233c13a092ec2da'], + }), + ('Lmoments', '1.2-3', { + 'checksums': ['e974b65d6116d540bc2c934c40c5552f64d7781b77c259a5b7724b1338c9e08e'], + }), + ('distillery', '1.0-4', { + 'checksums': ['3d3a8445471b19a6b652761ca783994b2d2108b64ff539b0597a9db9697d17d4'], + }), + ('extRemes', '2.0-8', { + 'checksums': ['d53d50d0feb6295f72c4f646242e1506ca51911c026f881d443d65f1c68ad75e'], + }), + ('pixmap', '0.4-11', { + 'checksums': ['6fa010749a59cdf56aad9f81271473b7d55697036203f2cd5d81372bcded7412'], + }), + ('tkrplot', '0.0-23', { + 'checksums': ['87a4323ce3bc6c852c2dae4727639b9a1c30724327a812379f21d73cecd7deb2'], + }), + ('misc3d', '0.8-4', { + 'checksums': ['75de3d2237f67f9e58a36e80a6bbf7e796d43eb46789f2dd1311270007bf5f62'], + }), + ('multicool', '0.1-10', { + 'checksums': [ + '5bb0cb0d9eb64420c862877247a79bb0afadacfe23262ec8c3fa26e5e34d6ff9', # multicool_0.1-10.tar.gz + ], + }), + ('plot3D', '1.1.1', { + 'checksums': ['f6fe4a001387132626fc553ed1d5720d448b8064eb5a6917458a798e1d381632'], + }), + ('plot3Drgl', '1.0.1', { + 'checksums': ['466d428d25c066c9c96d892f24da930513d42b1bdf76d3b53628c3ba13c3e48a'], + }), + ('OceanView', '1.0.4', { + 'checksums': ['e67f6f376737e1e5cf22fdfe2769a8f674e90c886b0e43942e97d9a3e6924f1c'], + }), + ('ks', '1.11.0', { + 'checksums': ['648e23578445049e4f73238b1c4b3a07e365c55577a9d8172cc69eaaf1377cf1'], + }), + ('logcondens', '2.1.5', { + 'checksums': ['72e61abc1f3eb28830266fbe5b0da0999eb5520586000a3024e7c26be93c02eb'], + }), + ('Iso', '0.0-17', { + 'checksums': ['c007d6eaf6335a15c1912b0804276ff39abce27b7a61539a91b8fda653629252'], + }), + ('penalized', '0.9-50', { + 'checksums': ['c12b3259e019f91c7bd02827ea3a27f842d9c15950fa6cc114dff23c89c297d1'], + }), + ('clusterRepro', '0.5-1.1', { + 'checksums': ['b7fcb9db0c762a2e6e22a0a0689affd73504c56f13c13b04272a946630334e6f'], + }), + ('randomForestSRC', '2.5.1', { + 'checksums': ['ad45878dab93cdf5fbdd88cbcf5e6cdcceb7fae6b9dd8d2ccddac2d6ce2faadc'], + }), + ('sm', '2.2-5.4', { + 'checksums': ['49f26c52728ac9dd2152d80ef1d3d59b98269bdc81616f81548fa4ed842ed842'], + }), + ('pbivnorm', '0.6.0', { + 'checksums': ['07c37d507cb8f8d2d9ae51a9a6d44dfbebd8a53e93c242c4378eaddfb1cc5f16'], + }), + ('lavaan', '0.5-23.1097', { + 'checksums': ['9aa7c3278f08f46b91fb0357dbdb9539936ba54e11d270d7febce0049efc9d87'], + }), + ('matrixcalc', '1.0-3', { + 'checksums': ['17e6caeeecd596b850a6caaa257984398de9ec5d2b41ce83c428f112614b9cb0'], + }), + ('arm', '1.9-3', { + 'checksums': ['1cefcc1d82431f1b3ed014ff04dd087fd0da3396df5a25144ffa80a8d01fe700'], + }), + ('mi', '1.0', { + 'checksums': ['34f44353101e8c3cb6bf59c5f4ff5b2391d884dcbb9d23066a11ee756b9987c0'], + }), + ('visNetwork', '2.0.3', { + 'checksums': ['bc2e75cf4cc1410d8eb528a38870666117e674f1b9ba5fa1ff769b8ab2e2462f'], + }), + ('rgexf', '0.15.3', { + 'checksums': ['2e8a7978d1fb977318e6310ba65b70a9c8890185c819a7951ac23425c6dc8147'], + }), + ('influenceR', '0.1.0', { + 'checksums': ['4fc9324179bd8896875fc0e879a8a96b9ef2a6cf42a296c3b7b4d9098519e98a'], + }), + ('downloader', '0.4', { + 'checksums': ['1890e75b028775154023f2135cafb3e3eed0fe908138ab4f7eff1fc1b47dafab'], + }), + ('DiagrammeR', '1.0.0', { + 'checksums': ['2b186dae1b19018681b979e9444bf16559c42740d8382676fbaf3b0f8a44337e'], + }), + ('sem', '3.1-9', { + 'checksums': ['4a33780202506543da85877cd2813250114420d6ec5e75457bc67477cd332cb9'], + }), + ('jpeg', '0.1-8', { + 'checksums': ['d032befeb3a414cefdbf70ba29a6c01541c54387cc0a1a98a4022d86cbe60a16'], + }), + ('network', '1.13.0', { + 'checksums': ['7a04ea89261cdf32ccb52222810699d5fca59a849053e306b5ec9dd5c1184f87'], + }), + ('statnet.common', '4.0.0', { + 'checksums': ['206e1967df661b277c6fde68f8b0bf4589508f569ff94f1ec5126c4c56a1867b'], + }), + ('sna', '2.4', { + 'checksums': ['2292b3190e8d879e494527ae9d9d1174c31cb4183749ecb455aedd8d534048cf'], + }), + ('glasso', '1.8', { + 'patches': [('glasso-1.8-ifort-no-fixed.patch', 1)], + 'checksums': [ + 'fc9ba74519388c194e14bae39d41f3fec8c2aade0177df364f61753f0fbf8a3d', # glasso_1.8.tar.gz + '87e966b6651c2d9ccd8a2c2ba842eef8dcbeaa3fdd25085bb1d5aff6e79f409c', # glasso-1.8-ifort-no-fixed.patch + ], + }), + ('huge', '1.2.7', { + 'checksums': ['042b771c334cf4d1a92c5c546ca025238919f772a50457594b7e0bd243498d8c'], + }), + ('d3Network', '0.5.2.1', { + 'checksums': ['5c798dc0c87c6d574abb7c1f1903346e6b0fec8adfd1df7aef5e4f9e7e3a09be'], + }), + ('ggm', '2.3', { + 'checksums': ['832ffe81ff87c6f1a6644e689ebbfb172924b4c4584ac8108d1244d153219ed8'], + }), + ('BDgraph', '2.44', { + 'checksums': ['06c3cbe72024d6f38329bed1393ef1e8c877fe2343cabe0c8cd8bd8b9cacb714'], + }), + ('qgraph', '1.4.4', { + 'checksums': ['f62a908a4185f30c2f6924a69f1a569a636fa3053de1e92288367b498b93f841'], + }), + ('HWxtest', '1.1.7', { + 'checksums': ['7cfcf7860d655945f9d3bbda4590374d3100bb5da6b49956f2e701b910a20e0c'], + }), + ('diveRsity', '1.9.90', { + 'checksums': ['b8f49cdbfbd82805206ad293fcb2dad65b962fb5523059a3e3aecaedf5c0ee86'], + }), + ('doSNOW', '1.0.16', { + 'checksums': ['161434ecd55f04d6b070da784b222a7686c914b73de558eef6048a229022398e'], + }), + ('phangorn', '2.4.0', { + 'checksums': ['31d0ea035b48d3940013f369e514351db19f9f92b2832c53f09f752b4a998875'], + }), + ('geepack', '1.2-1', { + 'checksums': ['7effe67381129a48154c445704490ea3b5f2e1adedb66cb65f61369dd1f8d38d'], + }), + ('biom', '0.3.12', { + 'checksums': ['4ad17f7811c7346dc4923bd6596a007c177eebb1944a9f46e5674afcc5fdd5a1'], + }), + ('pim', '2.0.1', { + 'checksums': ['174568a01f68b9601a4ea89ca5857bf4888242f00e4212bfb7a422d6292300d5'], + }), + ('minpack.lm', '1.2-1', { + 'checksums': ['14cb7dba3ef2b46da0479b46d46c76198e129a31f6157cd8b37f178adb15d5a3'], + }), + ('rootSolve', '1.7', { + 'checksums': ['08b3bb63f04fc0b065cb615b6ca1ef95eb6df7a813eb9eb625bc15c6de332c22'], + }), + ('diagram', '1.6.4', { + 'checksums': ['7c2bc5d5d634c3b8ca7fea79fb463e412962d88f47a77a74c811cc62f375ce38'], + }), + ('FME', '1.3.5', { + 'checksums': ['3619d88df2a41ca8819b93bb7dff3b8233f76ff8ab0ca67c664f530f835935e4'], + }), + ('bmp', '0.3', { + 'checksums': ['bdf790249b932e80bc3a188a288fef079d218856cf64ffb88428d915423ea649'], + }), + ('readbitmap', '0.1-4', { + 'checksums': ['2d45ddd1ee0eb7482d5d4a9cfe41b3aa645de8af89295b4b205d73b19ac6d821'], + }), + ('imager', '0.40.2', { + 'checksums': [ + '12be25495c32883961e2503c8064aa90473fc36046630f582ae28c1c06995c9d', # imager_0.40.2.tar.gz + ], + }), + ('signal', '0.7-6', { + 'checksums': ['6b60277b07cf0167f8272059b128cc82f27a9bab1fd33d74c2a9e1f2abca5def'], + }), + ('tuneR', '1.3.2', { + 'checksums': ['4aafd7d6330572711c117fa2d6e21e14485f695db38a7ebf5c7b3ba8723666f6'], + }), + ('pastecs', '1.3-18', { + 'checksums': ['5188662294bf91545d0c2e4d7de113296f5a8c2cbf38bdc2a90f3f7d03b3b447'], + }), + ('audio', '0.1-5', { + 'checksums': ['b4e229457a0a399b14136ac145e65bb007d9c8d46e421ae79fd26461450164c3'], + }), + ('fftw', '1.0-4', { + 'checksums': ['80413901ce751c0700ac53283366cfcfe3cbeec2982d29721a0275f9fb9de204'], + }), + ('seewave', '2.1.0', { + 'checksums': ['5ea4fd79fe99f094c6bb9092e6048490175e9bedcd6d6e97badc1143df861f44'], + }), + ('gsw', '1.0-5', { + 'checksums': ['eb468918ee91e429b47fbcac43269eca627b7f64b61520de5bbe8fa223e96453'], + }), + ('oce', '0.9-23', { + 'checksums': ['390fd082710ee1586074ff20df61208df4c76b9f2dc0c9b1125aade4c934b04c'], + }), + ('ineq', '0.2-13', { + 'checksums': ['e0876403f59a3dfc2ea7ffc0d965416e1ecfdecf154e5856e5f54800b3efda25'], + }), + ('soundecology', '1.3.3', { + 'checksums': ['276164d5eb92c78726c647be16232d2443acbf7061371ddde2672b4fdb7a069a'], + }), + ('memuse', '4.0-0', { + 'checksums': ['fbf8716a1388692ee439f69ac99643fa427eb100027d8911ff0fbfdcb5b6c3bc'], + }), + ('pinfsc50', '1.1.0', { + 'checksums': ['b6b9b6365a3f408533264d7ec820494f57eccaf362553e8478a46a8e5b474aba'], + }), + ('vcfR', '1.7.0', { + 'checksums': ['ba6bce3861d1c87d2746984e736a0cbb977fd5ac450995f143b322887ed1a4ef'], + }), + ('glmmML', '1.0.2', { + 'checksums': ['abc9ded054787f5459e0e419697927eb031f221be8e0cfdbf306f776d4b9bb59'], + }), + ('ucminf', '1.1-4', { + 'checksums': ['a2eb382f9b24e949d982e311578518710f8242070b3aa3314a331c1e1e7f6f07'], + }), + ('ordinal', '2015.6-28', { + 'checksums': ['fa33e29cc82bf241ad94fbbf5bb4dd6c9fe01803ba389957a4194d81e5979351'], + }), + ('Rtsne', '0.13', { + 'checksums': [ + '1c3bffe3bd11733ee4fe01749c293669daafda1af2ec74f9158f6080625b999d', # Rtsne_0.13.tar.gz + ], + }), + ('cowplot', '0.9.2', { + 'checksums': ['8b92ce7f92937fde06b0cfb86c7634a39b3b2101e362cc55c4bec6b3fde1d28f'], + }), + ('tsne', '0.1-3', { + 'checksums': ['66fdf5d73e69594af529a9c4f261d972872b9b7bffd19f85c1adcd66afd80c69'], + }), + ('pbapply', '1.3-4', { + 'checksums': ['cdfdaf9b8aecbe48daac858aecaf65a766b74a363d1eb7cd6ebf27c0549f6552'], + }), + ('RcppProgress', '0.4', { + 'checksums': ['3b1ecc82ced98eb481819a28737dac3658586e11ad16a92abd14c4649ae15e25'], + }), + ('sn', '1.5-1', { + 'checksums': ['fcfc077a2c1eb35b1ed875fea296b225540aefb05564cbb54477f266a0a2f850'], + }), + ('tclust', '1.3-1', { + 'checksums': ['fe4479a73b947d8f6c1cc63587283a8b6223d430d39eee4e5833a06d3d1726d2'], + }), + ('ranger', '0.9.0', { + 'checksums': ['17ecc45dae291f07c9a579bf05effe9d39dc70c75eefe4f5035422da6f9134de'], + }), + ('hexbin', '1.27.2', { + 'checksums': ['46d47b1efef75d6f126af686a4dd614228b60418b9a5bde9e9e5d11200a0ee52'], + }), + ('pryr', '0.1.4', { + 'checksums': ['d39834316504c49ecd4936cbbcaf3ee3dae6ded287af42475bf38c9e682f721b'], + }), + ('moments', '0.14', { + 'checksums': ['2a3b81e60dafdd092d2bdd3513d7038855ca7d113dc71df1229f7518382a3e39'], + }), + ('laeken', '0.4.6', { + 'checksums': ['465174263f2d495162bf1ee8ab35b362dae8088e458c162ce517813267d813e6'], + }), + ('VIM', '4.7.0', { + 'checksums': ['cdd64cbdca23c097efa8d5084bfc1c0d1449744e90a41680a5246db979d14cee'], + }), + ('proxy', '0.4-21', { + 'checksums': ['607770418758c7cb856c2e5da1e877270a60adc4a1f588588127edeff44330ee'], + }), + ('smoother', '1.1', { + 'checksums': ['91b55b82f805cfa1deedacc0a4e844a2132aa59df593f3b05676954cf70a195b'], + }), + ('dynamicTreeCut', '1.63-1', { + 'checksums': ['831307f64eddd68dcf01bbe2963be99e5cde65a636a13ce9de229777285e4db9'], + }), + ('DT', '0.4', { + 'checksums': ['3daa96b819ca54e5fbc2c7d78cb3637982a2d44be58cea0683663b71cfc7fa19'], + }), + ('beeswarm', '0.2.3', { + 'checksums': ['0115425e210dced05da8e162c8455526a47314f72e441ad2a33dcab3f94ac843'], + }), + ('vipor', '0.4.5', { + 'checksums': ['7d19251ac37639d6a0fed2d30f1af4e578785677df5e53dcdb2a22771a604f84'], + }), + ('ggbeeswarm', '0.6.0', { + 'checksums': ['bbac8552f67ff1945180fbcda83f7f1c47908f27ba4e84921a39c45d6e123333'], + }), + ('shinydashboard', '0.6.1', { + 'checksums': ['1ee38f257433d24455426bc9d85c36f588735a54fbf6143935fed9cccb3bf193'], + }), + ('rrcov', '1.4-3', { + 'checksums': ['d89631e0dfb39777af9fe303cc0537bbc82c6f3d2a1ed360de950c13dfc34f4d'], + }), + ('WriteXLS', '4.0.0', { + 'checksums': ['a0541da45e16bc4bf994cdf3f07a0e202c38d52386460c64e27fe6c1cd889d5b'], + }), + ('bst', '0.3-14', { + 'checksums': ['08013994d3ac79ffc78585cb2831d4d2e52f39423ba880f84c6224e4c6b6360b'], + }), + ('mpath', '0.3-4', { + 'checksums': ['2a77539924c1aaf9eece2277b415f1df7146c44f04886b4e96d2d9ad32b6c262'], + }), + ('timereg', '1.9.2', { + 'checksums': ['b0b969807e72003cc537c979f01b62e6199fa335baca4cf92473babcd19cac35'], + }), + ('peperr', '1.1-7', { + 'checksums': ['73e0422c71f2df59cd4a0f820c87dd828f2952b60df2d6c58f62a35559d74605'], + }), + ('heatmap3', '1.1.1', { + 'checksums': ['055e30a2fee0e8b6e499cdc5ccb7e37e5615ed3d52cc7058fc5ca5fc808cf393'], + }), + ('GlobalOptions', '0.0.12', { + 'checksums': ['c09da3f9b1646d0f815056cdbeb5fff7dda29f7dd8742d245f5f6dc7066077a9'], + }), + ('circlize', '0.4.3', { + 'checksums': ['ca768f40123262db745046a6209e59023cfd50af4d99bddc8ccffb3cdf21e95d'], + }), + ('GetoptLong', '0.1.6', { + 'checksums': ['f526f006e3ed8507f1f236430ac9e97341c1ee9c207fbb68f936dd4d377b28b5'], + }), + ('dendextend', '1.7.0', { + 'checksums': ['ad50970790561a661f0035e8f5e50943191755ff7c1d8a4befa3406b9bc23bcf'], + }), + ('RInside', '0.2.14', { + 'checksums': ['8de5340993fe879ca00fa559c5b1b27b408ba78bfc5f67d36d6f0b8d8e8649cf'], + }), + ('limSolve', '1.5.5.3', { + 'checksums': ['2f27c03411e0d771ad50d5412125bf4fa0ba461051610edc77e20d28488e86d2'], + }), + ('dbplyr', '1.2.1', { + 'checksums': ['b348e7a02623f037632c85fb11be16c40c01755ae6ca02c8c189cdc192a699db'], + }), + ('modelr', '0.1.1', { + 'checksums': ['25b95198d6aa23e28a0bd97dcdc78264ef168ae403928bff01e1ee81ca021ce7'], + }), + ('rematch', '1.0.1', { + 'checksums': ['a409dec978cd02914cdddfedc974d9b45bd2975a124d8870d52cfd7d37d47578'], + }), + ('cellranger', '1.1.0', { + 'checksums': ['5d38f288c752bbb9cea6ff830b8388bdd65a8571fd82d8d96064586bd588cf99'], + }), + ('readxl', '1.0.0', { + 'checksums': ['fbd62f07fed7946363698a57be88f4ef3fa254ecf456ef292535849c787fc7ad'], + }), + ('debugme', '1.1.0', { + 'checksums': ['4dae0e2450d6689a6eab560e36f8a7c63853abbab64994028220b8fd4b793ab1'], + }), + ('callr', '2.0.2', { + 'checksums': ['778595e3f0b08f4e33a3103bd8e84a183945074f9e7404cdee8d72b7d3b8a154'], + }), + ('clipr', '0.4.0', { + 'checksums': ['44a2f1ab4fde53e4fe81cf5800aa6ad45b72b5da93d6fe4d3661d7397220e8af'], + }), + ('reprex', '0.1.2', { + 'checksums': ['7a6fc5f2a8f48ca5c6829811b899671b861f3d17cbe98bf87d343a5cf54ead80'], + }), + ('selectr', '0.3-2', { + 'checksums': ['5e222b462b6d0ced877897da5cf2385128010c143979911e349f3c9c8991b94d'], + }), + ('rvest', '0.3.2', { + 'checksums': ['0d6e8837fb1df79b1c83e7b48d8f1e6245f34a10c4bb6952e7bec7867e4abb12'], + }), + ('tidyverse', '1.2.1', { + 'checksums': ['ad67a27bb4e89417a15338fe1a40251a7b5dedba60e9b72637963d3de574c37b'], + }), + ('R.cache', '0.13.0', { + 'checksums': ['d3d4a99a676734ea53e96747d87857fa69615e59858804e92f8ad9ddcf62c5c1'], + }), + ('R.rsp', '0.42.0', { + 'checksums': ['a02ebd3857849896f30993ed8306c88b03116250261d9d85dcee48103f0498fd'], + }), + ('listenv', '0.7.0', { + 'checksums': ['6126020b111870baea08b36afa82777cd578e88c17db5435cd137f11b3964555'], + }), + ('globals', '0.11.0', { + 'checksums': ['ac285bd040d02ddc230486a193f76fad78bb6f013577c702b0b58e9af6f3579f'], + }), + ('future', '1.7.0', { + 'checksums': ['382a2a7c5840ea86ba0c995fbbef37b9bde9e0e5754aa8a39e8bb4f047e1df51'], + }), + ('gdistance', '1.2-1', { + 'checksums': ['c1a74a86e31c26b6b1cd49c151c2e0ba362565667ec9971c08efc4194167cff3'], + }), + ('vioplot', '0.2', { + 'checksums': ['601f043630999e0498f0fba213d3d3fefd6ff0abf8fdb22119199b3d8d58939b'], + }), + ('emulator', '1.2-15', { + 'checksums': ['e221f185f610ca34d169c42dc560209094825ed0a4fe35db97892ca4ffc1e7e6'], + }), + ('gmm', '1.6-1', { + 'checksums': ['c1d6ac78cfa302895934fbefbf6d073bfdd5c0c92708bfe4a46fb7775804383e'], + }), + ('tmvtnorm', '1.4-10', { + 'checksums': ['1a9f35e9b4899672e9c0b263affdc322ecb52ec198b2bb015af9d022faad73f0'], + }), + ('IDPmisc', '1.1.17', { + 'checksums': ['18ec9db0aab1de526b8e57ac1f0223811806a814777149b793722b999e6f7c59'], + }), + ('gap', '1.1-21', { + 'checksums': ['fa94b64e3a9c77ff3b4bd5ef0faeb42e647bbaedf3127933bef30568cc5c546f'], + }), + ('qrnn', '2.0.2', { + 'checksums': ['a4f786f767c02d65e6200ed0688c4e99e415815f44a6e980103dbb695ffc8f70'], + }), + ('DHARMa', '0.1.5', { + 'checksums': ['97e3ad80583eb6612f59e225100a10364e39d23076e9a295c5f75c4aa1bffbd5'], + }), + ('bridgesampling', '0.4-0', { + 'checksums': ['9577b535535b46022d06a7372ee309e2eb2ef0d045d65e2f3ed507f9b88062bf'], + }), + ('BayesianTools', '0.1.4', { + 'checksums': ['ed0b68020a9f1b10eda4135a0734e2c88a09e7d3d1fd7b83772cdec1b680358e'], + }), + ('gomms', '1.0', { + 'checksums': ['52828c6fe9b78d66bde5474e45ff153efdb153f2bd9f0e52a20a668e842f2dc5'], + }), + ('feather', '0.3.1', { + 'checksums': ['f1069bf920e9bc3da6bf43542a3a7ccc3142544d759945115ecade69dd5ccde0'], + }), + ('tidyverse', '1.2.1', { + 'checksums': ['ad67a27bb4e89417a15338fe1a40251a7b5dedba60e9b72637963d3de574c37b'], + }), + ('dummies', '1.5.6', { + 'checksums': ['7551bc2df0830b98c53582cac32145d5ce21f5a61d97e2bb69fd848e3323c805'], + }), + ('SimSeq', '1.4.0', { + 'checksums': ['5ab9d4fe2cb1b7634432ff125a9e04d2f574fed06246a93859f8004e10790f19'], + }), + ('fdrtool', '1.2.15', { + 'checksums': ['65f964aa768d0703ceb7a199adc5e79ca79a6d29d7bc053a262eb533697686c0'], + }), + ('uniqueAtomMat', '0.1-3-2', { + 'checksums': ['f7024e73274e1e76a870ce5e26bd58f76e8f6df0aa9775c631b861d83f4f53d7'], + }), + ('PoissonSeq', '1.1.2', { + 'checksums': ['6f3dc30ad22e33e4fcfa37b3427c093d591c02f1b89a014d85e63203f6031dc2'], + }), + ('aod', '1.3', { + 'checksums': ['e377effe345987850ece985eabf79750ca1979d75469d17a323c21515ad1dda8'], + }), + ('cghFLasso', '0.2-1', { + 'checksums': ['6e697959b35a3ceb2baa1542ef81f0335006a5a9c937f0173c6483979cb4302c'], + }), + ('svd', '0.4.1', { + 'checksums': ['6f585cb622cc52e2b7f3efddb7a363e91771bff80b8facb554755c2b33b7f402'], + }), + ('Rssa', '1.0', { + 'checksums': ['9cc20a7101d8dff4c6cfb789f9bdc14e2b3bb128d7613a67b0f9633cf006902a'], + }), + ('JBTools', '0.7.2.9', { + 'checksums': ['b33cfa17339df7113176ad1832cbb0533acf5d25c36b95e888f561d586c5d62f'], + }), + ('RUnit', '0.4.31', { + 'checksums': ['9d764092216391c9d7e13bbe1585f5d00c357ed8b04c7e66ed82d229c34119cb'], + }), + ('DistributionUtils', '0.5-1', { + 'checksums': ['e92a29003d5e5974f53e40bdb8417e2bdabe784304e21360d7a1cbec7818853f'], + }), + ('gapfill', '0.9.6', { + 'checksums': ['850d0be9d05e3f3620f0f5143496321f1004ed966299bffd6a67a9abd8d9040d'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb index c99d8f02372..f4f158f939b 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb @@ -8,8 +8,8 @@ description = """R is a free software environment for statistical computing and toolchain = {'name': 'intel', 'version': '2018a'} -sources = [SOURCE_TAR_GZ] source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] checksums = ['b3e97d2fab7256d1c655c4075934725ba1cd7cb9237240a11bb22ccdad960337'] builddependencies = [ @@ -41,6 +41,7 @@ dependencies = [ ('NLopt', '2.4.2'), # for nloptr ('FFTW', '3.3.7'), # for fftw ('libsndfile', '1.0.28'), # for seewave + ('ICU', '61.1'), # for rJava & gdsfmt # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons # ('OpenSSL', '1.0.2h'), @@ -514,7 +515,7 @@ exts_list = [ 'checksums': ['d52b9e04b3291f9bda8a88c174678f520ddffc5f2edf9b3dfa6d97dca943ce9a'], }), ('foreign', '0.8-69', { - 'checksums': ['820e1409162fbd6418b80a0f5a4b50d649ee74f06d195a5210745619b16e1592'], + 'checksums': ['13689f5ec1ab09e8973be81c7f1799b7de4313176072887a9fa0b5825aed3468'], }), ('gam', '1.15', { 'checksums': ['1e365f9f328e018955140b4d842a30a499f4877291cb88cb9f147be79b62d1f0'], @@ -1080,7 +1081,11 @@ exts_list = [ 'checksums': ['c13ef1b6258e34ba53615b78f39dbe4d8ba47b976b3c24a3eedaecf5ffba19ed'], }), ('matrixStats', '0.53.1', { - 'checksums': ['df70bc9fb64716a7a633b5d0c2a2422b2c8d93ac5e64574528a325505df9712e'], + 'patches': ['matrixStats-0.53.1_O1.patch'], + 'checksums': [ + 'df70bc9fb64716a7a633b5d0c2a2422b2c8d93ac5e64574528a325505df9712e', # matrixStats_0.53.1.tar.gz + '96ef21a1d5ee4ccd1f4a6b74ef5aa2699a52c38b34613d8ff9f3c4af952aa8fd', # matrixStats-0.53.1_O1.patch + ], }), ('DiscriMiner', '0.1-29', { 'checksums': ['5aab7671086ef9940e030324651976456f0e84dab35edb7048693ade885228c6'], diff --git a/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb index da286fcbe09..d0174b6a763 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb @@ -8,8 +8,8 @@ description = """R is a free software environment for statistical computing and toolchain = {'name': 'iomkl', 'version': '2018a'} -sources = [SOURCE_TAR_GZ] source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] checksums = ['b3e97d2fab7256d1c655c4075934725ba1cd7cb9237240a11bb22ccdad960337'] builddependencies = [ @@ -41,6 +41,7 @@ dependencies = [ ('NLopt', '2.4.2'), # for nloptr ('FFTW', '3.3.7'), # for fftw ('libsndfile', '1.0.28'), # for seewave + ('ICU', '61.1'), # for rJava & gdsfmt # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons # ('OpenSSL', '1.0.2h'), @@ -514,7 +515,7 @@ exts_list = [ 'checksums': ['d52b9e04b3291f9bda8a88c174678f520ddffc5f2edf9b3dfa6d97dca943ce9a'], }), ('foreign', '0.8-69', { - 'checksums': ['820e1409162fbd6418b80a0f5a4b50d649ee74f06d195a5210745619b16e1592'], + 'checksums': ['13689f5ec1ab09e8973be81c7f1799b7de4313176072887a9fa0b5825aed3468'], }), ('gam', '1.15', { 'checksums': ['1e365f9f328e018955140b4d842a30a499f4877291cb88cb9f147be79b62d1f0'], @@ -1080,7 +1081,11 @@ exts_list = [ 'checksums': ['c13ef1b6258e34ba53615b78f39dbe4d8ba47b976b3c24a3eedaecf5ffba19ed'], }), ('matrixStats', '0.53.1', { - 'checksums': ['df70bc9fb64716a7a633b5d0c2a2422b2c8d93ac5e64574528a325505df9712e'], + 'patches': ['matrixStats-0.53.1_O1.patch'], + 'checksums': [ + 'df70bc9fb64716a7a633b5d0c2a2422b2c8d93ac5e64574528a325505df9712e', # matrixStats_0.53.1.tar.gz + '96ef21a1d5ee4ccd1f4a6b74ef5aa2699a52c38b34613d8ff9f3c4af952aa8fd', # matrixStats-0.53.1_O1.patch + ], }), ('DiscriMiner', '0.1-29', { 'checksums': ['5aab7671086ef9940e030324651976456f0e84dab35edb7048693ade885228c6'], diff --git a/easybuild/easyconfigs/r/R/matrixStats-0.53.1_O1.patch b/easybuild/easyconfigs/r/R/matrixStats-0.53.1_O1.patch new file mode 100644 index 00000000000..2defae6c7b0 --- /dev/null +++ b/easybuild/easyconfigs/r/R/matrixStats-0.53.1_O1.patch @@ -0,0 +1,20 @@ +force use of -O1 when compiling colCounts.c +workaround for "internal compiler error" when building with Intel compilers on an Intel Skylake system +author: B. Hajgato (Free University Brussels - VUB) +--- matrixStats.org/MD5 2018-02-11 15:13:37.000000000 +0100 ++++ matrixStats/MD5 2018-04-23 21:56:14.221226594 +0200 +@@ -278,6 +278,7 @@ + 536a4eddd5d389a2f37cac3702381be7 *src/x_OP_y.c + 5227137bc874290ef86b5d1b7e2878c2 *src/x_OP_y_lowlevel.h + ded428cafc1ea29e648f78a70297e459 *src/x_OP_y_lowlevel_template.h ++6d47ab21f006d1c9ed1582778c0d7f78 *src/Makevars + 8a7346f77a61c642a27791fa78ff9bb8 *tests/allocArray.R + d7014909df5dcc968e46e858a8c2686b *tests/allocMatrix.R + 508a5d07b8897d7c461cd73559a0c22f *tests/allocVector.R +--- matrixStats.org/src/Makevars 1970-01-01 01:00:00.000000000 +0100 ++++ matrixStats/src/Makevars 2018-04-23 21:55:46.953254629 +0200 +@@ -0,0 +1,4 @@ ++all: $(SHLIB) ++ ++colCounts.o : CFLAGS+=-O1 ++ diff --git a/easybuild/easyconfigs/r/RELION/RELION-2.1-foss-2018a.eb b/easybuild/easyconfigs/r/RELION/RELION-2.1-foss-2018a.eb new file mode 100644 index 00000000000..870a41642fa --- /dev/null +++ b/easybuild/easyconfigs/r/RELION/RELION-2.1-foss-2018a.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'RELION' +version = '2.1' + +homepage = 'http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page' +description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer + program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class + averages in electron cryo-microscopy (cryo-EM).""" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = ['https://github.com/3dem/relion/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['08729aac4fa0841e08df2c90a2c26cfe2aef52af2f5fb94a770ed2c11373b886'] + +builddependencies = [('CMake', '3.10.1')] + +dependencies = [ + ('X11', '20180131'), + ('FLTK', '1.3.4'), +] + +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-lpthread' " + +sanity_check_paths = { + 'files': ['bin/relion', 'lib/librelion_gui_lib.%s' % SHLIB_EXT, 'lib/librelion_lib.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/REMORA/REMORA-1.8.2-foss-2018a.eb b/easybuild/easyconfigs/r/REMORA/REMORA-1.8.2-foss-2018a.eb new file mode 100644 index 00000000000..d4c24d1e671 --- /dev/null +++ b/easybuild/easyconfigs/r/REMORA/REMORA-1.8.2-foss-2018a.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PackedBinary' + +name = 'REMORA' +version = '1.8.2' + +homepage = 'https://github.com/TACC/remora' +description = "REsource MOnitoring for Remote Applications" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = ['https://github.com/TACC/remora/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['140f71671787a49af822e97226c60db208b9ff6f3bf20556eac5b8c59e9fd42b'] + +install_cmd = 'cd remora-%(version)s && REMORA_INSTALL_PREFIX=%(installdir)s ./install.sh' + +sanity_check_paths = { + 'files': ['bin/mpstat', 'bin/remora', 'lib/libmpiP.a', 'lib/libmpiP.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextravars = {'REMORA_BIN': '%(installdir)s/bin'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/REMORA/REMORA-1.8.2-intel-2018a.eb b/easybuild/easyconfigs/r/REMORA/REMORA-1.8.2-intel-2018a.eb new file mode 100644 index 00000000000..9ca544d5aa4 --- /dev/null +++ b/easybuild/easyconfigs/r/REMORA/REMORA-1.8.2-intel-2018a.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PackedBinary' + +name = 'REMORA' +version = '1.8.2' + +homepage = 'https://github.com/TACC/remora' +description = "REsource MOnitoring for Remote Applications" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['https://github.com/TACC/remora/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['140f71671787a49af822e97226c60db208b9ff6f3bf20556eac5b8c59e9fd42b'] + +install_cmd = 'cd remora-%(version)s && REMORA_INSTALL_PREFIX=%(installdir)s ./install.sh' + +sanity_check_paths = { + 'files': ['bin/mpstat', 'bin/remora'], + 'dirs': [], +} + +modextravars = {'REMORA_BIN': '%(installdir)s/bin'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.3.0-intel-2017a.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.0-intel-2017a.eb index 743b20ec767..91d089bf8d2 100644 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.3.0-intel-2017a.eb +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.0-intel-2017a.eb @@ -12,7 +12,7 @@ source_urls = ['https://github.com/deweylab/RSEM/archive/'] sources = ['v%(version)s.tar.gz'] patches = ['RSEM-%(version)s_makefiles.patch'] checksums = [ - 'a6776aae25a690375504974d65e8554d6e3ddab93cef5b82969064854d22c09f', # v1.3.0.tar.gz + 'ecfbb79c23973e1c4134f05201f4bd89b0caf0ce4ae1ffd7c4ddc329ed4e05d2', # v1.3.0.tar.gz '2d244659206c78655b92f1bd519ee65f28a6b5f9418dfad04e887b64eca6641b', # RSEM-1.3.0_makefiles.patch ] diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.5.0-foss-2018a.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.5.0-foss-2018a.eb new file mode 100644 index 00000000000..f0ff53ef8fa --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.5.0-foss-2018a.eb @@ -0,0 +1,140 @@ +# With <3 for EasyBuild +# +# EasyConfig for Ruby 2.1: +# ---------------------------------------------------------------------------- +# Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Aaron Zauner +# ---------------------------------------------------------------------------- + +name = 'Ruby' +version = '2.5.0' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['46e6f3630f1888eb653b15fa811d77b5b1df6fd7a3af436b343cfe4f4503f2ab'] + +exts_default_options = { + 'source_urls': ['http://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +exts_list = [ + ('ffi', '1.9.18', { + 'checksums': ['a0df16d6a369a3306dd257adcb2ddef673e91b9740d0c5f77a98fde3ba288e0c'], + }), + ('childprocess', '0.8.0', { + 'checksums': ['bab28cef7c17bc9242d75c8dd535dd8d2bdc989d1c5cf02550b04b9cdfea3020'], + }), + ('json', '2.1.0', { + 'checksums': ['b76fd09b881088c6c64a12721a1528f2f747a1c2ee52fab4c1f60db8af946607'], + }), + ('cabin', '0.9.0', { + 'checksums': ['91c5394289e993e7037a6c869e3f212f31a5984d2b1811ac934f591c87446b2c'], + }), + ('backports', '3.11.0', { + 'checksums': ['df779df58c5cb157e69c504a046a8012503176349760d84d519b02f5b1605856'], + }), + ('arr-pm', '0.0.10', { + 'checksums': ['0fa2d425a84eeeaf8f95268568e826723b41aeefa14511d1f0ed1368c30bdd1f'], + }), + ('clamp', '1.1.2', { + 'checksums': ['f338133cf34d9a2b8d51d5b545f29c1455e5a3c631b62a4c19504ad50eb9a250'], + }), + ('multipart-post', '2.0.0', { + 'checksums': ['3dc44e50d3df3d42da2b86272c568fd7b75c928d8af3cc5f9834e2e5d9586026'], + }), + ('faraday', '0.13.1', { + 'checksums': ['1c82a788fb827fb4c01766e0777ed8044856f92f8824b7e3e6d663ba8fd4d8bf'], + }), + ('faraday_middleware', '0.12.2', { + 'checksums': ['2d90093c18c23e7f5a6f602ed3114d2c62abc3f7f959dd3046745b24a863f1dc'], + }), + ('highline', '1.7.10', { + 'checksums': ['1e147d5d20f1ad5b0e23357070d1e6d0904ae9f71c3c49e0234cf682ae3c2b06'], + }), + ('net-http-pipeline', '1.0.1', { + 'checksums': ['6923ce2f28bfde589a9f385e999395eead48ccfe4376d4a85d9a77e8c7f0b22f'], + }), + ('connection_pool', '2.2.1', { + 'checksums': ['870bfad9e390e2888f515210034223ae293fc3cbe77755e34251383f8d54779f'], + }), + ('net-http-persistent', '2.9.4', { + 'checksums': ['24274d207ffe66222ef70c78a052c7ea6e66b4ff21e2e8a99e3335d095822ef9'], + }), + ('multi_json', '1.12.2', { + 'checksums': ['5dcc0b569969f3d1658c68b5d597fcdc1fc3a34d4ae92b4615c740d95aaa51e5'], + }), + ('public_suffix', '3.0.1', { + 'checksums': ['67182699cb644e66b4c68d30b5f1dd42e3dfe6c0aa0d8fd36a1e71c97c6a7f57'], + }), + ('addressable', '2.4.0', { + 'checksums': ['7abfff765571b0a73549c9a9d2f7e143979cd0c252f7fa4c81e7102a973ef656'], + }), + ('gh', '0.15.1', { + 'checksums': ['ef733f81c17846f217f5ad9616105e9adc337775d41de1cc330133ad25708d3c'], + }), + ('launchy', '2.4.3', { + 'checksums': ['42f52ce12c6fe079bac8a804c66522a0eefe176b845a62df829defe0e37214a4'], + }), + ('ethon', '0.11.0', { + 'checksums': ['88ec7960a8e00f76afc96ed15dcc8be0cb515f963fe3bb1d4e0b5c51f9d7e078'], + }), + ('typhoeus', '1.3.0', { + 'checksums': ['d8d315e067ec9764c61727d77786a7a82309b43c3964416ef476ee65ac09ed06'], + }), + ('websocket', '1.2.5', { + 'checksums': ['c9de8b82226f9b4647522a9c73be4a1cd60b166b103c993717f94277cb453228'], + }), + ('pusher-client', '0.6.2', { + 'checksums': ['c405c931090e126c056d99f6b69a01b1bcb6cbfdde02389c93e7d547c6efd5a3'], + }), + ('diff-lcs', '1.3', { + 'checksums': ['ea7bf591567e391ef262a7c29edaf87c6205204afb5bb39dfa8f08f2e51282a3'], + }), + ('rspec-support', '3.7.0', { + 'checksums': ['77ec518aeb9d078b7a9db18c84afa51dd877398b1c0336275fb9c803e7c57743'], + }), + ('rspec-mocks', '3.7.0', { + 'checksums': ['23f7f0039e17f2841edfb51d678ac9e06c056903a7908db967f5618887f2022c'], + }), + ('rspec-expectations', '3.7.0', { + 'checksums': ['7e571848a5cbdb1661187d04e5c1f29287ec80fcb5a395f9994836892a3780bb'], + }), + ('rspec-core', '3.7.0', { + 'checksums': ['29a78669490cce51effb71693bbb7910b840dbf50fa91041bc30e9bde3ab8495'], + }), + ('rspec', '3.7.0', { + 'checksums': ['0174cfbed780e42aa181227af623e2ae37511f20a2fdfec48b54f6cf4d7a6404'], + }), + ('rack', '2.0.3', { + 'checksums': ['8c1c9bbafd74f11c78a29bd87c72a70e7b5b872712d1768ab83b33fec57d9fcd'], + }), + ('rack-protection', '2.0.0', { + 'checksums': ['5574f10cb3fcfe736389f121b868cd3320207aef777a34afb8f2d1226368aa11'], + }), + ('tilt', '2.0.8', { + 'checksums': ['2a3be6c56a8cc6338203c02910e20e858664b633adb550e1103804d75eae4000'], + }), + ('mustermann', '1.0.1', { + 'checksums': ['5b6ac679faa7e4de5de55d3d28e59c476f86e7f846a57754df75c9d6b685cd72'], + }), + ('sinatra', '2.0.0', { + 'checksums': ['51df699a50d394aa7b3920a4e8e1a3bb07f4c95515b580c9b4fa1a5019f27735'], + }), + ('rack-test', '0.8.2', { + 'checksums': ['4624f69a929b0ed030685249c0d2884876a221087c948c37b6cadcbeccd2683f'], + }), + ('bundler', '1.16.1', { + 'checksums': ['42b8e0f57093e1d10c15542f956a871446b759e7969d99f91caf3b6731c156e8'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.5-intel-2018a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.5-intel-2018a.eb new file mode 100644 index 00000000000..6b65c818285 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.5-intel-2018a.eb @@ -0,0 +1,19 @@ +name = 'SCOTCH' +version = '6.0.5' + +homepage = 'http://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'pic': True} + +source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] +checksums = ['f53f4d71a8345ba15e2dd4e102a35fd83915abf50ea73e1bf6efe1bc2b4220c7'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCons/SCons-3.0.1-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/s/SCons/SCons-3.0.1-foss-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..802e13353ed --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-3.0.1-foss-2018a-Python-2.7.14.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '3.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['24475e38d39c19683bc88054524df018fe6949d70fbd4c69e298d39a0269f173'] + +dependencies = [('Python', '2.7.14')] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': ['lib/%(namelower)s-%(version)s/%(name)s'], +} + +# no Python module to import during sanity check +options = {'modulename': False} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SCons/SCons-3.0.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/s/SCons/SCons-3.0.1-foss-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..1b3646d881e --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-3.0.1-foss-2018a-Python-3.6.4.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '3.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['24475e38d39c19683bc88054524df018fe6949d70fbd4c69e298d39a0269f173'] + +dependencies = [('Python', '3.6.4')] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': ['lib/%(namelower)s-%(version)s/%(name)s'], +} + +# no Python module to import during sanity check +options = {'modulename': False} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SCons/SCons-3.0.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/s/SCons/SCons-3.0.1-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..e215285c850 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-3.0.1-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '3.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['24475e38d39c19683bc88054524df018fe6949d70fbd4c69e298d39a0269f173'] + +dependencies = [('Python', '2.7.14')] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': ['lib/%(namelower)s-%(version)s/%(name)s'], +} + +# no Python module to import during sanity check +options = {'modulename': False} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SCons/SCons-3.0.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/s/SCons/SCons-3.0.1-intel-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..2681a9f309a --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-3.0.1-intel-2018a-Python-3.6.4.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '3.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['24475e38d39c19683bc88054524df018fe6949d70fbd4c69e298d39a0269f173'] + +dependencies = [('Python', '3.6.4')] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': ['lib/%(namelower)s-%(version)s/%(name)s'], +} + +# no Python module to import during sanity check +options = {'modulename': False} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SIMPLE/SIMPLE-2.5-foss-2018a.eb b/easybuild/easyconfigs/s/SIMPLE/SIMPLE-2.5-foss-2018a.eb new file mode 100644 index 00000000000..b46ae8ec1ec --- /dev/null +++ b/easybuild/easyconfigs/s/SIMPLE/SIMPLE-2.5-foss-2018a.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'SIMPLE' +version = '2.5' + +homepage = 'http://simplecryoem.com/' +description = """ Single-particle IMage Processing Linux Engine is a program package + for cryo-EM image processing, focusing on ab initio 3D reconstruction of low-symmetry single-particles. """ + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = ['http://simplecryoem.com/downloads'] +sources = ["%(namelower)s%(version)s.tgz"] +checksums = ['e3a25193151bf54eabebd5d775161ef6ae9996fa9c8d523649d26957cbc181b1'] + +builddependencies = [('CMake', '3.10.1')] + +separate_build_dir = True + +modextravars = { + 'SIMPLE_QSYS': 'local', + 'SIMPLE_PATH': '%(installdir)s', +} + +modextrapaths = {'PATH': 'scripts'} + +sanity_check_paths = { + 'files': ['bin/simple_distr_exec', 'bin/simple_exec', + 'lib/libSIMPLE%(version)s.a', 'lib/simple/simple_varlist.txt'], + 'dirs': ['scripts'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.8.3-foss-2017b.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.8.3-foss-2017b.eb new file mode 100644 index 00000000000..cc6d7ef2782 --- /dev/null +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.8.3-foss-2017b.eb @@ -0,0 +1,21 @@ +name = 'SLEPc' +version = '3.8.3' + +homepage = 'http://www.grycap.upv.es/slepc/' +description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution + of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for + either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a + partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://slepc.upv.es/download/distrib'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['60a10ba01151b904f68b52f6d5da5830acf5f82ad7d9778711e62ffcf82ec2ca'] + +dependencies = [('PETSc', '3.8.3', '-downloaded-deps')] + +petsc_arch = 'installed-arch-linux2-c-opt' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.12.0-foss-2016b.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.12.0-foss-2016b.eb new file mode 100644 index 00000000000..35c331c44b3 --- /dev/null +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.12.0-foss-2016b.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = "CMakeMake" + +name = 'SPAdes' +version = '3.12.0' + +homepage = 'http://cab.spbu.ru/software/spades/' +description = """Genome assembler for single-cell and isolates data sets""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['15b48a3bcbbe6a8ad58fd04ba5d3f1015990fbfd9bdf4913042803b171853ac7'] + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('libreadline', '6.3'), +] + +start_dir = 'src' + +separate_build_dir = True + +configopts = ' -DBoost_NO_BOOST_CMAKE=ON' + +sanity_check_commands = [('spades.py', '--test')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['spades-bwa', 'dipspades.py', 'spades-hammer', + 'spades-ionhammer', 'spades.py']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/STIR/STIR-3.0-intel-2018a.eb b/easybuild/easyconfigs/s/STIR/STIR-3.0-intel-2018a.eb new file mode 100644 index 00000000000..6caa15d09a5 --- /dev/null +++ b/easybuild/easyconfigs/s/STIR/STIR-3.0-intel-2018a.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'STIR' +version = '3.0' + +homepage = 'http://stir.sourceforge.net/' +description = "Software for Tomographic Image Reconstruction" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['https://github.com/UCL/STIR/archive/'] +sources = ['stir_rel_%(version_major)s_%(version_minor)s0.tar.gz'] +patches = ['STIR-%(version)s_fix-CMakeLists.patch'] +checksums = [ + '4d51ed5e8671f3de47b4fa215d8509a04ccd363c09a0e14b050c47d3e13a23e5', # stir_rel_3_00.tar.gz + 'd51690790e0cbd8b23e6abf6628658fa99ad151fa43a5f91ea9506d5744e1932', # STIR-3.0_fix-CMakeLists.patch +] + +builddependencies = [('CMake', '3.10.2')] +dependencies = [ + ('ncurses', '6.0'), + ('Boost', '1.66.0'), + ('X11', '20180131'), +] + +sanity_check_paths = { + 'files': ['bin/stir_divide', 'bin/stir_math', 'bin/stir_subtract'], + 'dirs': ['lib'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/STIR/STIR-3.0_fix-CMakeLists.patch b/easybuild/easyconfigs/s/STIR/STIR-3.0_fix-CMakeLists.patch new file mode 100644 index 00000000000..c279fff6485 --- /dev/null +++ b/easybuild/easyconfigs/s/STIR/STIR-3.0_fix-CMakeLists.patch @@ -0,0 +1,13 @@ +fix CMake error "An ELSEIF command was found after an ELSE command." +author: Kenneth Hoste (HPC-UGent) +--- STIR-stir_rel_3_00/src/display/CMakeLists.txt.orig 2018-05-18 18:42:00.493707771 +0200 ++++ STIR-stir_rel_3_00/src/display/CMakeLists.txt 2018-05-18 18:42:19.464021925 +0200 +@@ -29,7 +29,7 @@ + + elseif("${GRAPHICS}" STREQUAL "PGM") + ADD_DEFINITIONS(-DSTIR_PGM) +-else() ++#else() + # TODO + #ifeq "$(GRAPHICS)" "MATHLINK" + # this presumably needs a Mathlink library, depends on your system though diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-foss-2018a.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-foss-2018a.eb new file mode 100644 index 00000000000..d48d94e67f4 --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-foss-2018a.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '2.7.0' + +homepage = 'http://computation.llnl.gov/projects/sundials' +description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" + +toolchain = {'name': 'foss', 'version': '2018a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['http://computation.llnl.gov/projects/sundials/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d39fcac7175d701398e4eb209f7e92a5b30a78358d4a0c0fcc23db23c11ba104'] + +builddependencies = [('CMake', '3.10.2')] + +separate_build_dir = True + +configopts = "-DMPI_ENABLE=ON -DOPENMP_ENABLE=ON -DLAPACK_ENABLE=ON" + +solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] +sanity_check_paths = { + 'files': ['lib/libsundials_%s.a' % s for s in solvers + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + + ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in solvers + ['nvecopenmp', 'nvecparallel', 'nvecserial']], + 'dirs': ['examples/%s' % s for s in solvers] + ['include/%s' % s for s in solvers] + + ['examples/nvector', 'include/nvector', 'include/sundials'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-intel-2018a.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-intel-2018a.eb new file mode 100644 index 00000000000..9372ecfa47a --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-intel-2018a.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '2.7.0' + +homepage = 'http://computation.llnl.gov/projects/sundials' +description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['http://computation.llnl.gov/projects/sundials/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d39fcac7175d701398e4eb209f7e92a5b30a78358d4a0c0fcc23db23c11ba104'] + +builddependencies = [('CMake', '3.10.2')] + +separate_build_dir = True + +configopts = "-DMPI_ENABLE=ON -DOPENMP_ENABLE=ON -DLAPACK_ENABLE=ON" + +solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] +sanity_check_paths = { + 'files': ['lib/libsundials_%s.a' % s for s in solvers + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + + ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in solvers + ['nvecopenmp', 'nvecparallel', 'nvecserial']], + 'dirs': ['examples/%s' % s for s in solvers] + ['include/%s' % s for s in solvers] + + ['examples/nvector', 'include/nvector', 'include/sundials'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gimpic-2017b-OpenBLAS-0.2.20.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gimpic-2017b-OpenBLAS-0.2.20.eb new file mode 100644 index 00000000000..c4d1f2f7cf0 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gimpic-2017b-OpenBLAS-0.2.20.eb @@ -0,0 +1,22 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gimpic', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +checksums = ['0c74aeae690fe5ee4db7926f49c5d0bb69ce09eea75beb915e00bba07530395c'] + +blaslib = 'OpenBLAS' +blasver = '0.2.20' + +versionsuffix = "-%s-%s" % (blaslib, blasver) + +dependencies = [(blaslib, blasver, '', ('GCC', '6.4.0-2.28'))] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich-2017.08-OpenBLAS-0.2.20.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich-2017.08-OpenBLAS-0.2.20.eb new file mode 100644 index 00000000000..1d6b6b3961f --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich-2017.08-OpenBLAS-0.2.20.eb @@ -0,0 +1,22 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gmpich', 'version': '2017.08'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +checksums = ['0c74aeae690fe5ee4db7926f49c5d0bb69ce09eea75beb915e00bba07530395c'] + +blaslib = 'OpenBLAS' +blasver = '0.2.20' + +versionsuffix = "-%s-%s" % (blaslib, blasver) + +dependencies = [(blaslib, blasver)] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SimpleElastix/SimpleElastix-0.10.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/s/SimpleElastix/SimpleElastix-0.10.0-foss-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..2eee1939bbc --- /dev/null +++ b/easybuild/easyconfigs/s/SimpleElastix/SimpleElastix-0.10.0-foss-2018a-Python-3.6.4.eb @@ -0,0 +1,56 @@ +easyblock = 'CMakeMake' + +name = 'SimpleElastix' +version = '0.10.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://simpleelastix.github.io/' +description = " Multi-lingual medical image registration library. " + +toolchain = {'name': 'foss', 'version': '2018a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/SuperElastix/SimpleElastix/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['SimpleElastix-%(version)s_git-version.patch'] +checksums = [ + 'e4c08412a97871b171da2873e0ac76ab1ebfcf171c2d4a0958cc4b4f92a7b14b', # v0.10.0.tar.gz + 'fdb8d558ea295bda13b7483db0ec2a44def9e5066b794c42ae89a962c57804c7', # SimpleElastix-0.10.0_git-version.patch +] + +builddependencies = [('CMake', '3.10.2')] + +dependencies = [ + ('Python', '3.6.4'), +] + +configopts = '-DBUILD_EXAMPLES=OFF ' +configopts += '-DWRAP_TCL=OFF -DWRAP_LUA=OFF -DWRAP_RUBY=OFF -DWRAP_JAVA=OFF -DWRAP_CSHARP=OFF -DWRAP_R=OFF ' + +start_dir = 'SuperBuild' + +separate_build_dir = True + +skipsteps = ['install'] + +postinstallcmds = [ + # install SimpleITK Python wrapper: + "cd %(builddir)s/easybuild_obj/SimpleITK-build/Wrapping/Python/Packaging && " + + "python setup.py install --prefix=%(installdir)s", + # install elastix, ITK, and SimpleITK binaries: + 'mkdir -p %(installdir)s/bin && ' + + 'cp %(builddir)s/easybuild_obj/elastix-build/src/bin/* %(installdir)s/bin && ' + + 'cp %(builddir)s/easybuild_obj/ITK-build/bin/* %(installdir)s/bin && ' + + 'cp %(builddir)s/easybuild_obj/SimpleITK-build/bin/* %(installdir)s/bin' +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/SimpleITK-%(version_major_minor)s', 'lib', 'share'] +} + +sanity_check_commands = ["python -c 'import SimpleITK'"] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SimpleElastix/SimpleElastix-0.10.0_git-version.patch b/easybuild/easyconfigs/s/SimpleElastix/SimpleElastix-0.10.0_git-version.patch new file mode 100644 index 00000000000..9b502560dba --- /dev/null +++ b/easybuild/easyconfigs/s/SimpleElastix/SimpleElastix-0.10.0_git-version.patch @@ -0,0 +1,14 @@ +Do not check version from git repository +Author: Samuel Moors (Vrije Universiteit Brussel - VUB) +diff -ur SimpleElastix-0.10.0.orig/Version.cmake SimpleElastix-0.10.0/Version.cmake +--- SimpleElastix-0.10.0.orig/Version.cmake 2016-11-22 21:41:48.000000000 +0100 ++++ SimpleElastix-0.10.0/Version.cmake 2018-04-01 23:08:37.435509390 +0200 +@@ -14,7 +14,7 @@ + #set(SimpleITK_VERSION_TWEAK "") + + +-include(sitkSourceVersion) ++#include(sitkSourceVersion) + + # pre-release codes are defined based on suffix of most recent tags. + diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-2.0-foss-2018a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-2.0-foss-2018a.eb new file mode 100644 index 00000000000..9b58cd97365 --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-2.0-foss-2018a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'Stacks' +version = '2.0' + +homepage = 'http://creskolab.uoregon.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = ['http://catchenlab.life.illinois.edu/stacks/source/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a721b7367a9a342163e8d848d34616419a8c32e4be5ababfaa4f5d7c02d8cfa1'] + +dependencies = [ + ('zlib', '1.2.11'), + ('SAMtools', '1.7'), + ('sparsehash', '2.0.3'), +] + +configopts = "--enable-sparsehash" + +sanity_check_paths = { + 'files': ['bin/clone_filter', 'bin/cstacks', 'bin/gstacks', 'bin/kmer_filter', 'bin/phasedstacks', + 'bin/populations', 'bin/process_radtags', 'bin/process_shortreads', 'bin/sstacks', + 'bin/tsv2bam', 'bin/ustacks'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-2.0-intel-2018a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-2.0-intel-2018a.eb new file mode 100644 index 00000000000..912e5cdc597 --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-2.0-intel-2018a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'Stacks' +version = '2.0' + +homepage = 'http://creskolab.uoregon.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['http://catchenlab.life.illinois.edu/stacks/source/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a721b7367a9a342163e8d848d34616419a8c32e4be5ababfaa4f5d7c02d8cfa1'] + +dependencies = [ + ('zlib', '1.2.11'), + ('SAMtools', '1.7'), + ('sparsehash', '2.0.3'), +] + +configopts = "--enable-sparsehash" + +sanity_check_paths = { + 'files': ['bin/clone_filter', 'bin/cstacks', 'bin/gstacks', 'bin/kmer_filter', 'bin/phasedstacks', + 'bin/populations', 'bin/process_radtags', 'bin/process_shortreads', 'bin/sstacks', + 'bin/tsv2bam', 'bin/ustacks'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.1-foss-2018a-Python-3.6.4.eb index 537670455ad..f5893d1f18c 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.1-foss-2018a-Python-3.6.4.eb @@ -24,8 +24,9 @@ dependencies = [ exts_list = [ ('networkx', '2.1', { + 'source_tmpl': '%(name)s-%(version)s.zip', 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], - 'checksums': ['46aab610cdf15e680d944cafbf926a1d638f0cd2f1336b0f978b768a37d037f4'], + 'checksums': ['64272ca418972b70a196cb15d9c85a5a6041f09a2f32e0d30c0255f25d458bb1'], }), (name, version, { 'modulename': 'skimage', diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-foss-2017a-Python-2.7.13.eb new file mode 100644 index 00000000000..c5755d9fadf --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-foss-2017a-Python-2.7.13.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.16.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('matplotlib', '2.0.2', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intel-2018a-Python-3.6.4.eb new file mode 100755 index 00000000000..a6d836d4110 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intel-2018a-Python-3.6.4.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.19.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['5ca0ad32ee04abe0d4ba02c8d89d501b4e5e0304bdf4d45c2e9875a735b323a0'] + +dependencies = [ + ('Python', '3.6.4'), + ('matplotlib', '2.1.2', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-foss-2017a-Python-2.7.13.eb new file mode 100644 index 00000000000..30feb5a7a1f --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-foss-2017a-Python-2.7.13.eb @@ -0,0 +1,40 @@ +easyblock = 'Bundle' + +name = 'statsmodels' +version = '0.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://statsmodels.sourceforge.net/' +description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models, +and perform statistical tests.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [('Python', '2.7.13')] + +exts_list = [ + ('patsy', '0.4.1', { + 'source_tmpl': 'patsy-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], + 'checksums': ['dc1cc280045b0e6e50c04706fd1e26d2a00ea400aa112f88e8142f88b0b7d3d4'], + }), + (name, version, { + 'source_tmpl': 'statsmodels-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/statsmodels'], + 'checksums': ['4313dd4cbf1ebadef3661f6efd895132b615016e9bee560b5fdfd80c74dd422f'], + }), +] + +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.6.0_use_64b_alignment.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.6.0_use_64b_alignment.patch new file mode 100644 index 00000000000..258dad4878b --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.6.0_use_64b_alignment.patch @@ -0,0 +1,32 @@ +# Use 64 byte alignment. +# From https://github.com/tensorflow/tensorflow/pull/15606 +# Åke Sandgren, HPC2N +diff -ru tensorflow-1.6.0.orig/tensorflow/compiler/aot/runtime.h tensorflow-1.6.0/tensorflow/compiler/aot/runtime.h +--- tensorflow-1.6.0.orig/tensorflow/compiler/aot/runtime.h 2018-02-28 19:52:31.000000000 +0100 ++++ tensorflow-1.6.0/tensorflow/compiler/aot/runtime.h 2018-03-24 12:55:47.961694231 +0100 +@@ -26,7 +26,7 @@ + namespace runtime { + + // Align to 32-bytes, to mimic tensorflow::Allocator::kAllocatorAlignment. +-static constexpr size_t kAlign = 32; ++static constexpr size_t kAlign = 64; + + // aligned_buffer_bytes returns the sum of each size in `sizes`, skipping -1 + // values. There are `n` entries in `sizes`. Each buffer is aligned to kAlign +diff -ru tensorflow-1.6.0.orig/tensorflow/core/framework/allocator.h tensorflow-1.6.0/tensorflow/core/framework/allocator.h +--- tensorflow-1.6.0.orig/tensorflow/core/framework/allocator.h 2018-02-28 19:52:31.000000000 +0100 ++++ tensorflow-1.6.0/tensorflow/core/framework/allocator.h 2018-03-24 12:55:17.389840738 +0100 +@@ -67,13 +67,8 @@ + // device memory. + class Allocator { + public: +-#ifdef EIGEN_VECTORIZE_AVX512 + // Align to 64 byte boundary. + static constexpr size_t kAllocatorAlignment = 64; +-#else +- // Align to 32 byte boundary. +- static constexpr size_t kAllocatorAlignment = 32; +-#endif + + virtual ~Allocator(); + diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.7.0-foss-2018a-Python-3.6.4-CUDA-9.1.85.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.7.0-foss-2018a-Python-3.6.4-CUDA-9.1.85.eb new file mode 100644 index 00000000000..2672c150b35 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.7.0-foss-2018a-Python-3.6.4-CUDA-9.1.85.eb @@ -0,0 +1,40 @@ +name = 'TensorFlow' +version = '1.7.0' +cuda_ver = '9.1.85' +versionsuffix = '-Python-%%(pyver)s-CUDA-%s' % cuda_ver + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2018a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/tensorflow/tensorflow/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'TensorFlow-1.5.0_swig-env.patch', + 'TensorFlow-1.6.0_dont_expand_cuda_cudnn_path.patch', + 'TensorFlow-1.6.0_remove-msse-hardcoding.patch', + 'TensorFlow-1.6.0_lrt-flag.patch', +] +checksums = [ + 'c676a96fc8700722816b2b98c85578b2f99fac7a7b2484c9c7f0641484f8d50d', # v1.7.0.tar.gz + '53807290f1acb6a0f2a84f1a0ad9f917ee131c304b3e08679f3cbd335b22c7ef', # TensorFlow-1.5.0_swig-env.patch + # TensorFlow-1.6.0_dont_expand_cuda_cudnn_path.patch + 'f490b35179ed5c864255950784d5677d02f6c83a1684d406dbd31e2607d342fa', + '0ad82aab981721b1ed4881106d9accd43fe38b863ec147f6a16b278605012099', # TensorFlow-1.6.0_remove-msse-hardcoding.patch + 'd8b262eea9ff94c94c90b8c51219d8f56085ccee4370525cce8beba3b2b91d38', # TensorFlow-1.6.0_lrt-flag.patch +] + +builddependencies = [ + ('Bazel', '0.11.1'), + ('wheel', '0.30.0', '-Python-%(pyver)s'), +] +dependencies = [ + ('Python', '3.6.4'), + ('cuDNN', '7.0.5', '-CUDA-%s' % cuda_ver, True), +] + +cuda_compute_capabilities = ['3.0', '3.2', '3.5', '3.7', '5.0', '5.2', '5.3', '6.0', '6.1', '7.0'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.7.0_remove_DATE_defines.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.7.0_remove_DATE_defines.patch new file mode 100644 index 00000000000..5ec6b2797d7 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.7.0_remove_DATE_defines.patch @@ -0,0 +1,185 @@ +# Intel compiler don't allow redefinition of certain predefined macros. +# Both Bazel ands Tensorflow redfines __DATE__, __TIMESTAMP__, and __TIME__ +# +# This patch fixes the redfines in TF, but a similar patch is needed in +# Bazel. +# +# Åke Sandgren HPC2N +diff -ru tensorflow-1.7.0.orig/third_party/gpus/crosstool/CROSSTOOL_clang.tpl tensorflow-1.7.0/third_party/gpus/crosstool/CROSSTOOL_clang.tpl +--- tensorflow-1.7.0.orig/third_party/gpus/crosstool/CROSSTOOL_clang.tpl 2018-03-28 20:54:13.000000000 +0200 ++++ tensorflow-1.7.0/third_party/gpus/crosstool/CROSSTOOL_clang.tpl 2018-03-30 10:26:40.820330920 +0200 +@@ -61,14 +61,6 @@ + flag_set { + action: "c-compile" + action: "c++-compile" +- flag_group { +- # Make C++ compilation deterministic. Use linkstamping instead of these +- # compiler symbols. +- flag: "-Wno-builtin-macro-redefined" +- flag: "-D__DATE__=\"redacted\"" +- flag: "-D__TIMESTAMP__=\"redacted\"" +- flag: "-D__TIME__=\"redacted\"" +- } + } + } + +diff -ru tensorflow-1.7.0.orig/third_party/gpus/crosstool/CROSSTOOL_nvcc.tpl tensorflow-1.7.0/third_party/gpus/crosstool/CROSSTOOL_nvcc.tpl +--- tensorflow-1.7.0.orig/third_party/gpus/crosstool/CROSSTOOL_nvcc.tpl 2018-03-28 20:54:13.000000000 +0200 ++++ tensorflow-1.7.0/third_party/gpus/crosstool/CROSSTOOL_nvcc.tpl 2018-03-30 10:27:07.308199446 +0200 +@@ -75,13 +75,6 @@ + # Anticipated future default. + unfiltered_cxx_flag: "-no-canonical-prefixes" + +- # Make C++ compilation deterministic. Use linkstamping instead of these +- # compiler symbols. +- unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" +- + # Security hardening on by default. + # Conservative choice; -D_FORTIFY_SOURCE=2 may be unsafe in some cases. + # We need to undef it before redefining it as some distributions now have +@@ -191,12 +184,6 @@ + + # Anticipated future default. + unfiltered_cxx_flag: "-no-canonical-prefixes" +- # Make C++ compilation deterministic. Use linkstamping instead of these +- # compiler symbols. +- unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" + + # Security hardening on by default. + # Conservative choice; -D_FORTIFY_SOURCE=2 may be unsafe in some cases. +diff -ru tensorflow-1.7.0.orig/third_party/sycl/crosstool/CROSSTOOL.tpl tensorflow-1.7.0/third_party/sycl/crosstool/CROSSTOOL.tpl +--- tensorflow-1.7.0.orig/third_party/sycl/crosstool/CROSSTOOL.tpl 2018-03-28 20:54:13.000000000 +0200 ++++ tensorflow-1.7.0/third_party/sycl/crosstool/CROSSTOOL.tpl 2018-03-30 10:27:24.496114156 +0200 +@@ -69,13 +69,6 @@ + tool_path { name: "objdump" path: "/usr/bin/objdump" } + tool_path { name: "strip" path: "/usr/bin/strip" } + +- # Make C++ compilation deterministic. Use linkstamping instead of these +- # compiler symbols. +- unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" +- + compiler_flag: "-fPIE" + + # Keep stack frames for debugging, even in opt mode. +@@ -180,13 +173,6 @@ + tool_path { name: "objdump" path: "/usr/bin/objdump" } + tool_path { name: "strip" path: "/usr/bin/strip" } + +- # Make C++ compilation deterministic. Use linkstamping instead of these +- # compiler symbols. +- unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" +- + # All warnings are enabled. Maybe enable -Werror as well? + compiler_flag: "-Wall" + +@@ -214,4 +200,4 @@ + compiler_flag: "-O2" + compiler_flag: "-DNDEBUG" + } +-} +\ No newline at end of file ++} +diff -ru tensorflow-1.7.0.orig/third_party/toolchains/clang6/CROSSTOOL.tpl tensorflow-1.7.0/third_party/toolchains/clang6/CROSSTOOL.tpl +--- tensorflow-1.7.0.orig/third_party/toolchains/clang6/CROSSTOOL.tpl 2018-03-28 20:54:13.000000000 +0200 ++++ tensorflow-1.7.0/third_party/toolchains/clang6/CROSSTOOL.tpl 2018-03-30 10:27:35.736058390 +0200 +@@ -48,13 +48,6 @@ + + unfiltered_cxx_flag: "-no-canonical-prefixes" + +- # Make C++ compilation deterministic. Use linkstamping instead of these +- # compiler symbols. +- unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" +- + objcopy_embed_flag: "-I" + objcopy_embed_flag: "binary" + +diff -ru tensorflow-1.7.0.orig/third_party/toolchains/cpus/arm/CROSSTOOL.tpl tensorflow-1.7.0/third_party/toolchains/cpus/arm/CROSSTOOL.tpl +--- tensorflow-1.7.0.orig/third_party/toolchains/cpus/arm/CROSSTOOL.tpl 2018-03-28 20:54:13.000000000 +0200 ++++ tensorflow-1.7.0/third_party/toolchains/cpus/arm/CROSSTOOL.tpl 2018-03-30 10:28:03.343921449 +0200 +@@ -92,11 +92,6 @@ + cxx_flag: "/usr/include/" + linker_flag: "-lstdc++" + +- unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" +- + unfiltered_cxx_flag: "-no-canonical-prefixes" + unfiltered_cxx_flag: "-fno-canonical-system-headers" + +@@ -194,13 +189,6 @@ + unfiltered_cxx_flag: "-no-canonical-prefixes" + unfiltered_cxx_flag: "-fno-canonical-system-headers" + +- # Make C++ compilation deterministic. Use linkstamping instead of these +- # compiler symbols. +- unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" +- + # Security hardening on by default. + # Conservative choice; -D_FORTIFY_SOURCE=2 may be unsafe in some cases. + # We need to undef it before redefining it as some distributions now have +@@ -306,13 +294,6 @@ + # Anticipated future default. + unfiltered_cxx_flag: "-no-canonical-prefixes" + +- # Make C++ compilation deterministic. Use linkstamping instead of these +- # compiler symbols. +- unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" +- + # Security hardening on by default. + # Conservative choice; -D_FORTIFY_SOURCE=2 may be unsafe in some cases. + compiler_flag: "-D_FORTIFY_SOURCE=1" +@@ -411,13 +392,6 @@ + # Anticipated future default. + unfiltered_cxx_flag: "-no-canonical-prefixes" + +- # Make C++ compilation deterministic. Use linkstamping instead of these +- # compiler symbols. +- unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" +- + # Security hardening on by default. + # Conservative choice; -D_FORTIFY_SOURCE=2 may be unsafe in some cases. + # We need to undef it before redefining it as some distributions now have +diff -ru tensorflow-1.7.0.orig/third_party/toolchains/gpus/crosstool/CROSSTOOL tensorflow-1.7.0/third_party/toolchains/gpus/crosstool/CROSSTOOL +--- tensorflow-1.7.0.orig/third_party/toolchains/gpus/crosstool/CROSSTOOL 2018-03-28 20:54:13.000000000 +0200 ++++ tensorflow-1.7.0/third_party/toolchains/gpus/crosstool/CROSSTOOL 2018-03-30 10:28:19.359842027 +0200 +@@ -65,14 +65,6 @@ + flag_set { + action: "c-compile" + action: "c++-compile" +- flag_group { +- # Make C++ compilation deterministic. Use linkstamping instead of these +- # compiler symbols. +- flag: "-Wno-builtin-macro-redefined" +- flag: "-D__DATE__=\"redacted\"" +- flag: "-D__TIMESTAMP__=\"redacted\"" +- flag: "-D__TIME__=\"redacted\"" +- } + } + } + diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0-foss-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..3f885335e7c --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0-foss-2018a-Python-3.6.4.eb @@ -0,0 +1,35 @@ +name = 'TensorFlow' +version = '1.8.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = ['https://github.com/tensorflow/tensorflow/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'TensorFlow-1.5.0_swig-env.patch', + 'TensorFlow-%(version)s_remove-msse-hardcoding.patch', + 'TensorFlow-1.8.0_lrt-flag.patch', + 'TensorFlow-1.6.0_use_64b_alignment.patch', +] +checksums = [ + '47646952590fd213b747247e6870d89bb4a368a95ae3561513d6c76e44f92a75', # v1.8.0.tar.gz + '53807290f1acb6a0f2a84f1a0ad9f917ee131c304b3e08679f3cbd335b22c7ef', # TensorFlow-1.5.0_swig-env.patch + '4d043bba84d19aa38e402ef4ddaa89df936ae792f82693a49ce8ae4a1d091f6d', # TensorFlow-1.8.0_remove-msse-hardcoding.patch + '3c499788266800c71fa9874d411df79f7331320b3a86bc7c79c74763ae04c143', # TensorFlow-1.8.0_lrt-flag.patch + 'bcff66b5cc7a98e2ae894df6940aac5e3dcec3700773d24a6c3a5a69128ef66f', # TensorFlow-1.6.0_use_64b_alignment.patch +] + +builddependencies = [ + ('Bazel', '0.12.0'), + ('wheel', '0.31.0', versionsuffix), +] + +dependencies = [('Python', '3.6.4')] + +preconfigopts = 'export CC_OPT_FLAGS="$CC_OPT_FLAGS -mno-avx512f" && ' + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0-intel-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..3c201e2bfe7 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0-intel-2018a-Python-3.6.4.eb @@ -0,0 +1,43 @@ +name = 'TensorFlow' +version = '1.8.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['https://github.com/tensorflow/tensorflow/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'TensorFlow-1.5.0_swig-env.patch', + 'TensorFlow-%(version)s_icc-fixes.patch', + 'TensorFlow-%(version)s_remove-msse-hardcoding.patch', + 'TensorFlow-1.6.0_use_64b_alignment.patch', + 'TensorFlow-1.7.0_remove_DATE_defines.patch', + 'TensorFlow-%(version)s_no_grpc.patch', + 'TensorFlow-%(version)s_no_boringssl.patch', + 'TensorFlow-%(version)s_lrt-flag.patch', +] +checksums = [ + '47646952590fd213b747247e6870d89bb4a368a95ae3561513d6c76e44f92a75', # v1.8.0.tar.gz + '53807290f1acb6a0f2a84f1a0ad9f917ee131c304b3e08679f3cbd335b22c7ef', # TensorFlow-1.5.0_swig-env.patch + '05f8e5c186407a03dd325bfc969d745959b5fa12a92dad3dba8168beb4b8da98', # TensorFlow-1.8.0_icc-fixes.patch + '4d043bba84d19aa38e402ef4ddaa89df936ae792f82693a49ce8ae4a1d091f6d', # TensorFlow-1.8.0_remove-msse-hardcoding.patch + 'bcff66b5cc7a98e2ae894df6940aac5e3dcec3700773d24a6c3a5a69128ef66f', # TensorFlow-1.6.0_use_64b_alignment.patch + '7e946d54f93a310816173c8a925d4a9f1f46f200fc6b87d628916312efc6f01b', # TensorFlow-1.7.0_remove_DATE_defines.patch + '7cb51ce3b4619320cb1c6ef4ff1d4e1afcc5b41254c7031fccf51e3e7ce34844', # TensorFlow-1.8.0_no_grpc.patch + 'ca2338e189496711bc8798070d63255c3ff77ed616d1d2775abbef6f984db7ad', # TensorFlow-1.8.0_no_boringssl.patch + '3c499788266800c71fa9874d411df79f7331320b3a86bc7c79c74763ae04c143', # TensorFlow-1.8.0_lrt-flag.patch +] + +builddependencies = [ + ('Bazel', '0.11.1'), + ('wheel', '0.30.0', versionsuffix), +] + +dependencies = [('Python', '3.6.4')] + +preconfigopts = 'env CC_OPT_FLAGS="$CC_OPT_FLAGS -U__AVX512F__" ' + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0_icc-fixes.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0_icc-fixes.patch new file mode 100644 index 00000000000..9bf30ae8cce --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0_icc-fixes.patch @@ -0,0 +1,3163 @@ +fix issues to get TensorFlow to compile with Intel compilers +* disable use of -Werror +* enable use of -DSQLITE_DISABLE_INTRINSIC for SQLite build +* fix syntax for template function calls; + generated changes via Perl regex commands, see also https://github.com/tensorflow/tensorflow/issues/9496) +author: Kenneth Hoste (HPC-UGent) +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/coder/kernels/range_coder_ops_test.cc tensorflow-1.8.0/tensorflow/contrib/coder/kernels/range_coder_ops_test.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/coder/kernels/range_coder_ops_test.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/coder/kernels/range_coder_ops_test.cc 2018-04-30 17:56:17.973036089 +0200 +@@ -220,7 +220,7 @@ + const Eigen::array broadcast = {1, 32, 32, 16, 1}; + + Tensor cdf{DT_INT32, {1, 32, 32, 16, kMaxValue + 2}}; +- cdf.tensor() = temp.tensor().broadcast(broadcast); ++ cdf.template tensor() = temp.template tensor().broadcast(broadcast); + + TestEncodeAndDecode(kPrecision, data, cdf); + } +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/factorization/kernels/wals_solver_ops.cc tensorflow-1.8.0/tensorflow/contrib/factorization/kernels/wals_solver_ops.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/factorization/kernels/wals_solver_ops.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/factorization/kernels/wals_solver_ops.cc 2018-04-30 17:56:27.760976435 +0200 +@@ -116,7 +116,7 @@ + context->allocate_output( + 0, TensorShape({block_size, factor_dim, factor_dim}), + &output_lhs_tensor)); +- auto output_lhs_t = output_lhs_tensor->tensor(); ++ auto output_lhs_t = output_lhs_tensor->template tensor(); + output_lhs_t.setZero(); + Tensor* output_rhs_tensor; + OP_REQUIRES_OK(context, context->allocate_output( +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/ffmpeg/decode_audio_op.cc tensorflow-1.8.0/tensorflow/contrib/ffmpeg/decode_audio_op.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/ffmpeg/decode_audio_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/ffmpeg/decode_audio_op.cc 2018-04-30 17:56:28.548971633 +0200 +@@ -82,7 +82,7 @@ + OP_REQUIRES_OK(context, + context->allocate_output( + 0, TensorShape({frame_count, channel_count}), &output)); +- auto matrix = output->tensor(); ++ auto matrix = output->template tensor(); + for (int32 frame = 0; frame < frame_count; ++frame) { + for (int32 channel = 0; channel < channel_count; ++channel) { + matrix(frame, channel) = output_samples[frame * channel_count + channel]; +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/fused_conv/kernels/fused_conv2d_bias_activation_op.cc tensorflow-1.8.0/tensorflow/contrib/fused_conv/kernels/fused_conv2d_bias_activation_op.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/fused_conv/kernels/fused_conv2d_bias_activation_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/fused_conv/kernels/fused_conv2d_bias_activation_op.cc 2018-04-30 17:56:30.288961031 +0200 +@@ -269,8 +269,8 @@ + TF_RETURN_IF_ERROR(ctx->allocate_temp(DataTypeToEnum::value, nchw_shape, + transformed_tensor)); + functor::NHWCToNCHW()( +- ctx->eigen_device(), nhwc_tensor.tensor(), +- transformed_tensor->tensor()); ++ ctx->eigen_device(), nhwc_tensor.template tensor(), ++ transformed_tensor->template tensor()); + } else { + // If depth <= 1, then just reshape. + CHECK(transformed_tensor->CopyFrom(nhwc_tensor, nchw_shape)); +@@ -492,8 +492,8 @@ + FORMAT_OIHW, filter_param.shape(), FORMAT_HWIO), + &maybe_transformed_filter)); + functor::TransformFilter()( +- ctx->eigen_device(), To32Bit(filter_param.tensor()), +- To32Bit(maybe_transformed_filter.tensor())); ++ ctx->eigen_device(), To32Bit(filter_param.template tensor()), ++ To32Bit(maybe_transformed_filter.template tensor())); + filter = &maybe_transformed_filter; + } + +@@ -612,8 +612,8 @@ + if (!is_int8x4 && (data_format == FORMAT_NHWC) && (output_depth > 1)) { + functor::NCHWToNHWC()( + ctx->eigen_device(), +- const_cast(output)->tensor(), +- output_param->tensor()); ++ const_cast(output)->template tensor(), ++ output_param->template tensor()); + } + } + +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/image/kernels/bipartite_match_op.cc tensorflow-1.8.0/tensorflow/contrib/image/kernels/bipartite_match_op.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/image/kernels/bipartite_match_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/image/kernels/bipartite_match_op.cc 2018-04-30 17:56:33.732940046 +0200 +@@ -86,7 +86,7 @@ + &column_to_row_match_indices)); + + TTypes::ConstTensor distance_mat = +- input_distance_mat.shaped( ++ input_distance_mat.template shaped( + {num_input_rows, num_input_columns}); + + // Greedy bi-partite matching. +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/image/kernels/image_ops.cc tensorflow-1.8.0/tensorflow/contrib/image/kernels/image_ops.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/image/kernels/image_ops.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/image/kernels/image_ops.cc 2018-04-30 17:56:33.760939875 +0200 +@@ -80,11 +80,11 @@ + ProjectiveGenerator::kNumParameters), + errors::InvalidArgument( + "Input transform should be num_images x 8 or 1 x 8")); +- auto images = images_t.tensor(); ++ auto images = images_t.template tensor(); + auto transform = transform_t.matrix(); + Tensor* output_t; + OP_REQUIRES_OK(ctx, ctx->allocate_output(0, images_t.shape(), &output_t)); +- auto output = output_t->tensor(); ++ auto output = output_t->template tensor(); + (FillProjectiveTransform(interpolation_))( + ctx->eigen_device(), &output, images, transform); + } +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/image/kernels/segmentation_ops.cc tensorflow-1.8.0/tensorflow/contrib/image/kernels/segmentation_ops.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/image/kernels/segmentation_ops.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/image/kernels/segmentation_ops.cc 2018-04-30 17:56:33.860939266 +0200 +@@ -56,11 +56,11 @@ + // itself. + TensorRangeFunctor()(ctx->eigen_device(), + forest_t.flat()); +- auto rank = rank_t.tensor(); ++ auto rank = rank_t.template tensor(); + rank.device(ctx->eigen_device()) = rank.constant(OutputType(0)); + +- const auto images = images_t.tensor(); +- auto forest = forest_t.tensor(); ++ const auto images = images_t.template tensor(); ++ auto forest = forest_t.template tensor(); + ImageConnectedComponentsFunctor()( + ctx, output_t->flat(), images, forest, rank); + } +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/pi_examples/camera/camera.cc tensorflow-1.8.0/tensorflow/contrib/pi_examples/camera/camera.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/pi_examples/camera/camera.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/pi_examples/camera/camera.cc 2018-04-30 17:57:02.928762224 +0200 +@@ -346,7 +346,7 @@ + tensorflow::DT_FLOAT, + tensorflow::TensorShape( + {1, wanted_height, wanted_width, wanted_channels})); +- auto image_tensor_mapped = image_tensor.tensor(); ++ auto image_tensor_mapped = image_tensor.template tensor(); + tensorflow::uint8* in = image_data; + float* out = image_tensor_mapped.data(); + const size_t image_rowlen = image_width * image_channels; +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/pi_examples/label_image/label_image.cc tensorflow-1.8.0/tensorflow/contrib/pi_examples/label_image/label_image.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/pi_examples/label_image/label_image.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/pi_examples/label_image/label_image.cc 2018-04-30 17:57:03.000761786 +0200 +@@ -157,7 +157,7 @@ + tensorflow::DT_FLOAT, + tensorflow::TensorShape( + {1, wanted_height, wanted_width, wanted_channels})); +- auto image_tensor_mapped = image_tensor.tensor(); ++ auto image_tensor_mapped = image_tensor.template tensor(); + tensorflow::uint8* in = image_data.data(); + float* out = image_tensor_mapped.data(); + const size_t image_rowlen = image_width * image_channels; +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/seq2seq/kernels/beam_search_ops.cc tensorflow-1.8.0/tensorflow/contrib/seq2seq/kernels/beam_search_ops.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/seq2seq/kernels/beam_search_ops.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/seq2seq/kernels/beam_search_ops.cc 2018-04-30 17:57:06.728739089 +0200 +@@ -80,12 +80,12 @@ + max_sequence_lengths.shape().DebugString())); + Tensor* beams; + OP_REQUIRES_OK(ctx, ctx->allocate_output(0, step_ids_shape, &beams)); +- typename TTypes::ConstTensor step_ids_t(step_ids.tensor()); +- typename TTypes::ConstTensor parent_ids_t(parent_ids.tensor()); ++ typename TTypes::ConstTensor step_ids_t(step_ids.template tensor()); ++ typename TTypes::ConstTensor parent_ids_t(parent_ids.template tensor()); + typename TTypes::ConstVec max_seq_lens_t = + max_sequence_lengths.vec(); + typename TTypes::ConstScalar end_token_t(end_token.scalar()); +- typename TTypes::Tensor beams_t(beams->tensor()); ++ typename TTypes::Tensor beams_t(beams->template tensor()); + const T end_token_value = end_token_t(); + functor::GatherTree()(ctx, device, step_ids_t, parent_ids_t, + max_seq_lens_t, end_token_value, beams_t); +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/tensorboard/db/summary_converter.cc tensorflow-1.8.0/tensorflow/contrib/tensorboard/db/summary_converter.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/tensorboard/db/summary_converter.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/tensorboard/db/summary_converter.cc 2018-04-30 17:57:12.788702200 +0200 +@@ -258,7 +258,7 @@ + if (tensor.dtype() == DT_UINT8) { + // For uint8 input, no normalization is necessary + auto ith_image = [&tensor, batch_size, hw, depth](int i) { +- auto values = tensor.shaped({batch_size, hw, depth}); ++ auto values = tensor.template shaped({batch_size, hw, depth}); + return typename TTypes::ConstMatrix( + &values(i, 0, 0), Eigen::DSizes(hw, depth)); + }; +@@ -304,7 +304,7 @@ + sa->set_content_type("audio/wav"); + + auto values = +- tensor.shaped({batch_size, length_frames, num_channels}); ++ tensor.template shaped({batch_size, length_frames, num_channels}); + auto channels_by_frames = typename TTypes::ConstMatrix( + &values(i, 0, 0), + Eigen::DSizes(length_frames, num_channels)); +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/hybrid/core/ops/hard_routing_function_op.cc tensorflow-1.8.0/tensorflow/contrib/tensor_forest/hybrid/core/ops/hard_routing_function_op.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/hybrid/core/ops/hard_routing_function_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/tensor_forest/hybrid/core/ops/hard_routing_function_op.cc 2018-04-30 17:57:10.620715397 +0200 +@@ -127,12 +127,12 @@ + OP_REQUIRES_OK( + context, context->allocate_output(1, output_path_shape, &output_path)); + +- auto out_probability = output_probability->tensor(); +- auto out_path = output_path->tensor(); ++ auto out_probability = output_probability->template tensor(); ++ auto out_path = output_path->template tensor(); + +- const auto data = input_data.tensor(); +- const auto tree_parameters = tree_parameters_tensor.tensor(); +- const auto tree_biases = tree_biases_tensor.tensor(); ++ const auto data = input_data.template tensor(); ++ const auto tree_parameters = tree_parameters_tensor.template tensor(); ++ const auto tree_biases = tree_biases_tensor.template tensor(); + + // Deterministically traverse the tree to a leaf. + for (int i = 0; i < num_data; i++) { +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/hybrid/core/ops/k_feature_gradient_op.cc tensorflow-1.8.0/tensorflow/contrib/tensor_forest/hybrid/core/ops/k_feature_gradient_op.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/hybrid/core/ops/k_feature_gradient_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/tensor_forest/hybrid/core/ops/k_feature_gradient_op.cc 2018-04-30 17:57:10.640715275 +0200 +@@ -134,14 +134,14 @@ + tensorforest::Initialize(*out_data, 0.0f); + + // Compute output. +- const auto input_data = input_data_tensor.tensor(); +- const auto tree_parameters = tree_parameters_tensor.tensor(); +- const auto tree_biases = tree_biases_tensor.tensor(); +- const auto routes = routing_tensor.tensor(); ++ const auto input_data = input_data_tensor.template tensor(); ++ const auto tree_parameters = tree_parameters_tensor.template tensor(); ++ const auto tree_biases = tree_biases_tensor.template tensor(); ++ const auto routes = routing_tensor.template tensor(); + +- auto routes_grad = out_routes->tensor(); +- auto data_grad = out_data->tensor(); +- auto weights_grad = out_weights->tensor(); ++ auto routes_grad = out_routes->template tensor(); ++ auto data_grad = out_data->template tensor(); ++ auto weights_grad = out_weights->template tensor(); + + std::vector feature_set; + for (int i = 0; i < num_data; i++) { +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/hybrid/core/ops/k_feature_routing_function_op.cc tensorflow-1.8.0/tensorflow/contrib/tensor_forest/hybrid/core/ops/k_feature_routing_function_op.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/hybrid/core/ops/k_feature_routing_function_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/tensor_forest/hybrid/core/ops/k_feature_routing_function_op.cc 2018-04-30 17:57:10.664715129 +0200 +@@ -125,8 +125,8 @@ + OP_REQUIRES_OK(context, context->allocate_output(0, output_shape, + &output_probabilities)); + +- auto out_probs = output_probabilities->tensor(); +- const auto tree_biases = tree_biases_tensor.tensor(); ++ auto out_probs = output_probabilities->template tensor(); ++ const auto tree_biases = tree_biases_tensor.template tensor(); + + // Iteratively compute the probability of reaching each leaf. + std::vector feature_set; +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/hybrid/core/ops/routing_function_op.cc tensorflow-1.8.0/tensorflow/contrib/tensor_forest/hybrid/core/ops/routing_function_op.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/hybrid/core/ops/routing_function_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/tensor_forest/hybrid/core/ops/routing_function_op.cc 2018-04-30 17:57:10.688714983 +0200 +@@ -110,8 +110,8 @@ + OP_REQUIRES_OK(context, context->allocate_output(0, output_shape, + &output_probabilities)); + +- auto out_probs = output_probabilities->tensor(); +- const auto tree_biases = tree_biases_tensor.tensor(); ++ auto out_probs = output_probabilities->template tensor(); ++ const auto tree_biases = tree_biases_tensor.template tensor(); + + // Iteratively compute the probability of reaching each leaf. + for (int i = 0; i < num_data; i++) { +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/hybrid/core/ops/routing_gradient_op.cc tensorflow-1.8.0/tensorflow/contrib/tensor_forest/hybrid/core/ops/routing_gradient_op.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/hybrid/core/ops/routing_gradient_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/tensor_forest/hybrid/core/ops/routing_gradient_op.cc 2018-04-30 17:57:10.712714837 +0200 +@@ -108,9 +108,9 @@ + + OP_REQUIRES_OK(context, context->allocate_output(0, output_shape, &output)); + +- auto out = output->tensor(); +- const auto tree_biases = tree_biases_tensor.tensor(); +- const auto routes = routing_tensor.tensor(); ++ auto out = output->template tensor(); ++ const auto tree_biases = tree_biases_tensor.template tensor(); ++ const auto routes = routing_tensor.template tensor(); + + // A derivation of the gradient can be found at go/routingderivation. + for (int i = 0; i < num_data; i++) { +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/hybrid/core/ops/stochastic_hard_routing_function_op.cc tensorflow-1.8.0/tensorflow/contrib/tensor_forest/hybrid/core/ops/stochastic_hard_routing_function_op.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/hybrid/core/ops/stochastic_hard_routing_function_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/tensor_forest/hybrid/core/ops/stochastic_hard_routing_function_op.cc 2018-04-30 17:57:10.736714690 +0200 +@@ -140,9 +140,9 @@ + OP_REQUIRES_OK( + context, context->allocate_output(1, output_path_shape, &output_path)); + +- auto out_probability = output_probability->tensor(); +- auto out_path = output_path->tensor(); +- const auto tree_biases = tree_biases_tensor.tensor(); ++ auto out_probability = output_probability->template tensor(); ++ auto out_path = output_path->template tensor(); ++ const auto tree_biases = tree_biases_tensor.template tensor(); + + // Stochastically traverse the tree to a leaf. + +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/hybrid/core/ops/stochastic_hard_routing_gradient_op.cc tensorflow-1.8.0/tensorflow/contrib/tensor_forest/hybrid/core/ops/stochastic_hard_routing_gradient_op.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/hybrid/core/ops/stochastic_hard_routing_gradient_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/tensor_forest/hybrid/core/ops/stochastic_hard_routing_gradient_op.cc 2018-04-30 17:57:10.756714569 +0200 +@@ -163,16 +163,16 @@ + tensorforest::Initialize(*output_parameters, 0.0); + tensorforest::Initialize(*output_bias, 0.0); + +- auto out_routing = output_routing->tensor(); +- auto out_data = output_data->tensor(); +- auto out_parameters = output_parameters->tensor(); +- auto out_bias = output_bias->tensor(); ++ auto out_routing = output_routing->template tensor(); ++ auto out_data = output_data->template tensor(); ++ auto out_parameters = output_parameters->template tensor(); ++ auto out_bias = output_bias->template tensor(); + +- const auto data = input_data.tensor(); +- const auto tree_parameters = tree_parameters_tensor.tensor(); +- const auto tree_biases = tree_biases_tensor.tensor(); +- const auto path_probability = path_probability_tensor.tensor(); +- const auto path = path_tensor.tensor(); ++ const auto data = input_data.template tensor(); ++ const auto tree_parameters = tree_parameters_tensor.template tensor(); ++ const auto tree_biases = tree_biases_tensor.template tensor(); ++ const auto path_probability = path_probability_tensor.template tensor(); ++ const auto path = path_tensor.template tensor(); + + for (int i = 0; i < num_data; i++) { + const Tensor point = input_data.Slice(i, i + 1); +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/hybrid/core/ops/unpack_path_op.cc tensorflow-1.8.0/tensorflow/contrib/tensor_forest/hybrid/core/ops/unpack_path_op.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/hybrid/core/ops/unpack_path_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/tensor_forest/hybrid/core/ops/unpack_path_op.cc 2018-04-30 17:57:10.780714423 +0200 +@@ -91,10 +91,10 @@ + tensorforest::Initialize(*output, 0.0f); + VLOG(1) << "unpack after init"; + +- auto out = output->tensor(); ++ auto out = output->template tensor(); + +- const auto path = path_tensor.tensor(); +- const auto path_values = path_values_tensor.tensor(); ++ const auto path = path_tensor.template tensor(); ++ const auto path_values = path_values_tensor.template tensor(); + + for (int i = 0; i < num_data; i++) { + for (int j = 0; j < tree_depth; j++) { +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/kernels/model_ops.cc tensorflow-1.8.0/tensorflow/contrib/tensor_forest/kernels/model_ops.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/kernels/model_ops.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/tensor_forest/kernels/model_ops.cc 2018-04-30 17:57:11.372710819 +0200 +@@ -197,7 +197,7 @@ + output_shape.AddDim(num_outputs); + OP_REQUIRES_OK(context, context->allocate_output(0, output_shape, + &output_predictions)); +- TTypes::Tensor out = output_predictions->tensor(); ++ TTypes::Tensor out = output_predictions->template tensor(); + + std::vector tree_paths( + param_proto_.inference_tree_paths() ? num_data : 0); +@@ -297,7 +297,7 @@ + OP_REQUIRES_OK(context, context->allocate_output(0, output_shape, + &output_predictions)); + +- auto leaf_ids = output_predictions->tensor(); ++ auto leaf_ids = output_predictions->template tensor(); + + auto set_leaf_ids = [&leaf_ids](int32 i, int32 id) { leaf_ids(i) = id; }; + +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/kernels/scatter_add_ndim_op.cc tensorflow-1.8.0/tensorflow/contrib/tensor_forest/kernels/scatter_add_ndim_op.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/kernels/scatter_add_ndim_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/tensor_forest/kernels/scatter_add_ndim_op.cc 2018-04-30 17:57:11.444710381 +0200 +@@ -63,7 +63,7 @@ + + auto input = input_tensor.flat(); + +- const auto indices = indices_tensor.tensor(); ++ const auto indices = indices_tensor.template tensor(); + const auto deltas = deltas_tensor.unaligned_flat(); + + const int32 num_dims = +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/kernels/tree_utils.cc tensorflow-1.8.0/tensorflow/contrib/tensor_forest/kernels/tree_utils.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/kernels/tree_utils.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/tensor_forest/kernels/tree_utils.cc 2018-04-30 17:57:11.540709797 +0200 +@@ -175,8 +175,8 @@ + // unhelpful compiler errors when trying something that seems sane. This + // helps us do a simple thing like access the first element (the counts) + // of these tensors so we can calculate expected value in Variance(). +- const auto splits_count_accessor = split_sums.tensor(); +- const auto totals_count_accessor = total_sums.tensor(); ++ const auto splits_count_accessor = split_sums.template tensor(); ++ const auto totals_count_accessor = total_sums.template tensor(); + + Eigen::array bcast; + bcast[0] = num_splits; +@@ -238,8 +238,8 @@ + const int32 num_classes = + static_cast(split_counts.shape().dim_size(2)) - 1; + +- auto tc = total_counts.tensor(); +- auto lc = split_counts.tensor(); ++ auto tc = total_counts.template tensor(); ++ auto lc = split_counts.template tensor(); + + int n = tc(accumulator, 0); + +@@ -349,8 +349,8 @@ + const int32 num_classes = + static_cast(split_counts.shape().dim_size(2)) - 1; + +- auto tc = total_counts.tensor(); +- auto lc = split_counts.tensor(); ++ auto tc = total_counts.template tensor(); ++ auto lc = split_counts.template tensor(); + + double leftc = 0.0; + double leftc2 = 0.0; +@@ -377,8 +377,8 @@ + static_cast(split_counts.shape().dim_size(2)) - 1; + + mu->resize(num_classes * 2); +- auto tc = total_counts.tensor(); +- auto lc = split_counts.tensor(); ++ auto tc = total_counts.template tensor(); ++ auto lc = split_counts.template tensor(); + + double total = tc(accumulator, 0); + +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/kernels/tree_utils_test.cc tensorflow-1.8.0/tensorflow/contrib/tensor_forest/kernels/tree_utils_test.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/kernels/tree_utils_test.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/tensor_forest/kernels/tree_utils_test.cc 2018-04-30 17:57:11.584709529 +0200 +@@ -58,7 +58,7 @@ + + Initialize(t, 42.0); + +- const auto vals = t.tensor(); ++ const auto vals = t.template tensor(); + EXPECT_FLOAT_EQ(vals(0, 0), 42); + EXPECT_FLOAT_EQ(vals(1, 1), 42); + EXPECT_FLOAT_EQ(vals(3, 0), 42); +diff -ru tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/kernels/v4/input_data.cc tensorflow-1.8.0/tensorflow/contrib/tensor_forest/kernels/v4/input_data.cc +--- tensorflow-1.8.0.orig/tensorflow/contrib/tensor_forest/kernels/v4/input_data.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/contrib/tensor_forest/kernels/v4/input_data.cc 2018-04-30 17:57:11.960707240 +0200 +@@ -106,14 +106,14 @@ + const Tensor& sparse_values, + const Tensor& sparse_shape) { + if (dense.shape().dims() == 2) { +- dense_data_.reset(new DenseStorageType(dense.tensor())); ++ dense_data_.reset(new DenseStorageType(dense.template tensor())); + } + if (sparse_indices.shape().dims() == 2) { + sparse_indices_.reset( +- new SparseIndicesStorageType(sparse_indices.tensor())); ++ new SparseIndicesStorageType(sparse_indices.template tensor())); + sparse_values_.reset( +- new SparseValuesStorageType(sparse_values.tensor())); +- sparse_batch_size_ = sparse_shape.tensor()(0); ++ new SparseValuesStorageType(sparse_values.template tensor())); ++ sparse_batch_size_ = sparse_shape.template tensor()(0); + } + original_dense_tensor_ = dense; + } +diff -ru tensorflow-1.8.0.orig/tensorflow/core/framework/tensor.h tensorflow-1.8.0/tensorflow/core/framework/tensor.h +--- tensorflow-1.8.0.orig/tensorflow/core/framework/tensor.h 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/framework/tensor.h 2018-04-30 17:58:04.340388612 +0200 +@@ -232,9 +232,9 @@ + /// typedef float T; + /// Tensor my_mat(...built with Shape{rows: 3, cols: 5}...); + /// auto mat = my_mat.matrix(); // 2D Eigen::Tensor, 3 x 5. +- /// auto mat = my_mat.tensor(); // 2D Eigen::Tensor, 3 x 5. ++ /// auto mat = my_mat.template tensor(); // 2D Eigen::Tensor, 3 x 5. + /// auto vec = my_mat.vec(); // CHECK fails as my_mat is 2D. +- /// auto vec = my_mat.tensor(); // CHECK fails as my_mat is 2D. ++ /// auto vec = my_mat.template tensor(); // CHECK fails as my_mat is 2D. + /// auto mat = my_mat.matrix();// CHECK fails as type mismatch. + /// + /// ``` +@@ -289,11 +289,11 @@ + /// // 2D Eigen::Tensor 12 x 5: + /// auto inner = my_ten.flat_inner_dims(); + /// // 2D Eigen::Tensor 4 x 15: +- /// auto outer = my_ten.shaped({4, 15}); ++ /// auto outer = my_ten.template shaped({4, 15}); + /// // CHECK fails, bad num elements: +- /// auto outer = my_ten.shaped({4, 8}); ++ /// auto outer = my_ten.template shaped({4, 8}); + /// // 3D Eigen::Tensor 6 x 5 x 2: +- /// auto weird = my_ten.shaped({6, 5, 2}); ++ /// auto weird = my_ten.template shaped({6, 5, 2}); + /// // CHECK fails, type mismatch: + /// auto bad = my_ten.flat(); + /// +diff -ru tensorflow-1.8.0.orig/tensorflow/core/framework/tensor_test.cc tensorflow-1.8.0/tensorflow/core/framework/tensor_test.cc +--- tensorflow-1.8.0.orig/tensorflow/core/framework/tensor_test.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/framework/tensor_test.cc 2018-04-30 17:58:04.652386716 +0200 +@@ -350,7 +350,7 @@ + EXPECT_TRUE(t.shape().IsSameSize(TensorShape({2, 3, 4, 5}))); + EXPECT_TRUE(zero_t.shape().IsSameSize(TensorShape({3, 0, 2, 0, 5}))); + +- auto tensor = t.tensor(); ++ auto tensor = t.template tensor(); + EXPECT_EQ(2, tensor.dimension(0)); + EXPECT_EQ(3, tensor.dimension(1)); + EXPECT_EQ(4, tensor.dimension(2)); +@@ -465,9 +465,9 @@ + } + + TEST_F(TensorReshapeTest, ReshapeError) { +- EXPECT_DEATH((t.shaped({})), "1 vs. 120"); +- EXPECT_DEATH((t.shaped({119})), "119 vs. 120"); +- EXPECT_DEATH((t.shaped({2, 3, 4, 6})), "144 vs. 120"); ++ EXPECT_DEATH((t.template shaped({})), "1 vs. 120"); ++ EXPECT_DEATH((t.template shaped({119})), "119 vs. 120"); ++ EXPECT_DEATH((t.template shaped({2, 3, 4, 6})), "144 vs. 120"); + + EXPECT_DEATH((t.unaligned_shaped({})), "1 vs. 120"); + EXPECT_DEATH((t.unaligned_shaped({119})), "119 vs. 120"); +@@ -720,9 +720,9 @@ + LOG(INFO) << "reinterpret_last_dimension"; + { + Tensor t_nchw_vect_c(DT_QINT8, TensorShape({2, 3, 5, 7, 4})); +- auto nchw_vect_c = t_nchw_vect_c.tensor(); ++ auto nchw_vect_c = t_nchw_vect_c.template tensor(); + Tensor t_expected_nchw(DT_INT32, TensorShape({2, 3, 5, 7})); +- auto expected_nchw = t_expected_nchw.tensor(); ++ auto expected_nchw = t_expected_nchw.template tensor(); + int8 val = 0; + for (int n = 0; n < t_nchw_vect_c.shape().dim_size(0); ++n) { + for (int c = 0; c < t_nchw_vect_c.shape().dim_size(1); ++c) { +@@ -835,9 +835,9 @@ + EXPECT_TRUE(t.shape().IsSameSize(TensorShape({10, 4, 3, 2}))); + + // Get the N dimensional tensor (N==4 here) +- auto e_t = t.tensor(); ++ auto e_t = t.template tensor(); + // Reshape to view it as a two-dimensional tensor +- auto e_2d = t.shaped({10, 4 * 3 * 2}); ++ auto e_2d = t.template shaped({10, 4 * 3 * 2}); + for (int i = 0; i < 10; i++) { + // Assign a 1 x 4*3*2 matrix (really vector) to a slice of size + // 1 x 4*3*2 in e_t. +@@ -1165,8 +1165,8 @@ + // A simple slice along dim0. + Tensor y = x.Slice(4, 8); + EXPECT_TRUE(y.shape().IsSameSize(TensorShape({4, 4, 34}))); +- auto tx = x.tensor(); +- auto ty = y.tensor(); ++ auto tx = x.template tensor(); ++ auto ty = y.template tensor(); + for (int i = 0; i < 4; ++i) { + for (int j = 0; j < 4; ++j) { + for (int k = 0; k < 34; ++k) { +@@ -1183,7 +1183,7 @@ + + // A slice of a slice. + auto z = x.Slice(4, 8).Slice(2, 3); +- auto tz = z.tensor(); ++ auto tz = z.template tensor(); + EXPECT_EQ(1, z.dim_size(0)); + for (int j = 0; j < 4; ++j) { + for (int k = 0; k < 34; ++k) { +@@ -1196,7 +1196,7 @@ + } + { + EXPECT_EQ(1, saved.dim_size(0)); +- auto tsaved = saved.tensor(); ++ auto tsaved = saved.template tensor(); + for (int j = 0; j < 4; ++j) { + for (int k = 0; k < 34; ++k) { + EXPECT_EQ(tsaved(0, j, k), 6.0); +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/adjust_contrast_op.cc tensorflow-1.8.0/tensorflow/core/kernels/adjust_contrast_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/adjust_contrast_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/adjust_contrast_op.cc 2018-04-30 17:58:11.528344921 +0200 +@@ -78,9 +78,9 @@ + const int64 batch = input.NumElements() / (height * width * channels); + const int64 shape[4] = {batch, height, width, channels}; + functor::AdjustContrast()( +- context->eigen_device(), input.shaped(shape), ++ context->eigen_device(), input.template shaped(shape), + factor.scalar(), min_value.scalar(), +- max_value.scalar(), mean_values.shaped(shape), ++ max_value.scalar(), mean_values.template shaped(shape), + output->shaped(shape)); + } + } +@@ -214,7 +214,7 @@ + TensorShape({batch, channels}), &mean_values)); + // TODO(zhengxq): for multiple batches, shard them into different batches. + auto input_data = input->shaped({batch, image_size, channels}); +- auto mean_data = mean_values.tensor(); ++ auto mean_data = mean_values.template tensor(); + auto output_data = output->shaped({batch, image_size, channels}); + + // Calculate the mean of the inputs. +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/argmax_op.cc tensorflow-1.8.0/tensorflow/core/kernels/argmax_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/argmax_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/argmax_op.cc 2018-04-30 17:58:11.896342684 +0200 +@@ -79,8 +79,8 @@ + #define HANDLE_DIM(NDIM) \ + case NDIM: \ + ArgFunctor::Reduce##NDIM(context->eigen_device(), \ +- input.tensor(), axis, \ +- output->tensor()); \ ++ input.template tensor(), axis, \ ++ output->template tensor()); \ + break; + + switch (input_dims) { +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/attention_ops.cc tensorflow-1.8.0/tensorflow/core/kernels/attention_ops.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/attention_ops.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/attention_ops.cc 2018-04-30 17:58:12.012341979 +0200 +@@ -59,8 +59,8 @@ + "input must be a vector of size 2 (height, width)", + window_size.shape().DebugString())); + +- const int64 output_height = window_size.tensor()(0); +- const int64 output_width = window_size.tensor()(1); ++ const int64 output_height = window_size.template tensor()(0); ++ const int64 output_width = window_size.template tensor()(1); + TensorShape output_shape = input_shape; + output_shape.set_dim(1, output_height); + output_shape.set_dim(2, output_width); +@@ -87,16 +87,16 @@ + std::vector > offset_vec; + offset_vec.reserve(batch_size); + for (int i = 0; i < batch_size; ++i) { +- float offset_y = offsets.tensor()(i, 0); +- float offset_x = offsets.tensor()(i, 1); ++ float offset_y = offsets.template tensor()(i, 0); ++ float offset_x = offsets.template tensor()(i, 1); + // Eigen::ExtractGlimpses expects offsets as (x,y), whereas the + // calling TensorFlow operates with (y,x) as indices. + offset_vec.push_back(Eigen::IndexPair(offset_x, offset_y)); + } + +- output->tensor().swap_layout().device( ++ output->template tensor().swap_layout().device( + context->eigen_cpu_device()) = +- Eigen::ExtractGlimpses(input.tensor().swap_layout(), ++ Eigen::ExtractGlimpses(input.template tensor().swap_layout(), + output_width, output_height, offset_vec, + normalized_, centered_, uniform_noise_); + } +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/avgpooling_op.cc tensorflow-1.8.0/tensorflow/core/kernels/avgpooling_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/avgpooling_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/avgpooling_op.cc 2018-04-30 17:58:12.036341833 +0200 +@@ -166,8 +166,8 @@ + context->allocate_output(0, output_shape, &output)); + Eigen::PaddingType pt = BrainPadding2EigenPadding(padding_); + functor::SpatialAvgPooling()( +- context->eigen_device(), output->tensor(), +- tensor_in.tensor(), params.window_rows, params.window_cols, ++ context->eigen_device(), output->template tensor(), ++ tensor_in.template tensor(), params.window_rows, params.window_cols, + params.row_stride, params.col_stride, pt); + } + } +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/batch_kernels.cc tensorflow-1.8.0/tensorflow/core/kernels/batch_kernels.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/batch_kernels.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/batch_kernels.cc 2018-04-30 17:58:12.184340933 +0200 +@@ -69,7 +69,7 @@ + } + if (input.NumElements() > 0) { + inputs_flat.emplace_back(new typename TTypes::ConstMatrix( +- input.shaped({1, input.NumElements()}))); ++ input.template shaped({1, input.NumElements()}))); + } + output_dim0 += input.dim_size(0); + } +@@ -146,7 +146,7 @@ + suffix_dim_size *= input.shape().dim_size(i); + } + auto input_reshaped = +- input.shaped({input.shape().dim_size(0), suffix_dim_size}); ++ input.template shaped({input.shape().dim_size(0), suffix_dim_size}); + + int64 position = 0; + for (const int64 size : sizes) { +@@ -155,7 +155,7 @@ + Tensor output; + TF_RETURN_IF_ERROR( + context->allocate_temp(input.dtype(), output_shape, &output)); +- auto output_shaped = output.shaped({size, suffix_dim_size}); ++ auto output_shaped = output.template shaped({size, suffix_dim_size}); + + Eigen::DSizes slice_indices{position, 0}; + Eigen::DSizes slice_sizes{size, suffix_dim_size}; +@@ -632,7 +632,7 @@ + std::vector split_inputs; + if (nonempty_input) { + auto batch_indices = +- batch_index_t.shaped({batch_index_t.dim_size(0), 3}); ++ batch_index_t.template shaped({batch_index_t.dim_size(0), 3}); + for (int i = 0; i < batch_index_t.dim_size(0); ++i) { + sizes.push_back(batch_indices(i, 2) - batch_indices(i, 1)); + batch_keys.push_back(batch_indices(i, 0)); +@@ -828,7 +828,7 @@ + EXCLUSIVE_LOCKS_REQUIRED(mu_) { + const Tensor& batch_index_t = context->input(1); + auto batch_index = +- batch_index_t.shaped({batch_index_t.dim_size(0), 3}); ++ batch_index_t.template shaped({batch_index_t.dim_size(0), 3}); + std::vector tensors; + for (int i = 0; i < batch_index_t.dim_size(0); ++i) { + auto available_it = available_tensors_.find(batch_index(i, 0)); +@@ -878,7 +878,7 @@ + } + std::unordered_set missing_tensors; + const auto batch_index = +- batch_index_t.shaped({batch_index_t.dim_size(0), 3}); ++ batch_index_t.template shaped({batch_index_t.dim_size(0), 3}); + for (int i = 0; i < batch_index_t.dim_size(0); ++i) { + const int64 batch_key = batch_index(i, 0); + if (available_tensors_.find(batch_key) == available_tensors_.end()) { +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/batch_matmul_op_impl.h tensorflow-1.8.0/tensorflow/core/kernels/batch_matmul_op_impl.h +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/batch_matmul_op_impl.h 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/batch_matmul_op_impl.h 2018-04-30 17:58:12.232340641 +0200 +@@ -67,7 +67,7 @@ + struct ParallelMatMulKernel { + static void Conjugate(const OpKernelContext* context, Tensor* out) { + const Eigen::ThreadPoolDevice d = context->eigen_cpu_device(); +- auto z = out->tensor(); ++ auto z = out->template tensor(); + z.device(d) = z.conjugate(); + } + +@@ -75,9 +75,9 @@ + const Tensor in_y, bool adj_x, bool adj_y, Tensor* out, + int start, int limit) { + static_assert(IsComplex, "Complex type expected."); +- auto Tx = in_x.tensor(); +- auto Ty = in_y.tensor(); +- auto Tz = out->tensor(); ++ auto Tx = in_x.template tensor(); ++ auto Ty = in_y.template tensor(); ++ auto Tz = out->template tensor(); + // We use the identities + // conj(a) * conj(b) = conj(a * b) + // conj(a) * b = conj(a * conj(b)) +@@ -110,9 +110,9 @@ + static void Run(const OpKernelContext* context, const Tensor& in_x, + const Tensor& in_y, bool adj_x, bool adj_y, Tensor* out, + int start, int limit) { +- auto Tx = in_x.tensor(); +- auto Ty = in_y.tensor(); +- auto Tz = out->tensor(); ++ auto Tx = in_x.template tensor(); ++ auto Ty = in_y.template tensor(); ++ auto Tz = out->template tensor(); + Eigen::array, 1> contract_pairs; + contract_pairs[0] = ContractionDims(adj_x, adj_y); + const Eigen::ThreadPoolDevice d = context->eigen_cpu_device(); +@@ -410,9 +410,9 @@ + static void Run(const OpKernelContext* context, const Tensor& in_x, + const Tensor& in_y, bool adj_x, bool adj_y, Tensor* out, + int start, int limit) { +- auto Tx = in_x.tensor(); +- auto Ty = in_y.tensor(); +- auto Tz = out->tensor(); ++ auto Tx = in_x.template tensor(); ++ auto Ty = in_y.template tensor(); ++ auto Tz = out->template tensor(); + Eigen::array, 1> contract_pairs; + contract_pairs[0] = ContractionDims(adj_x, adj_y); + auto d = context->eigen_sycl_device(); +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/batch_norm_op.cc tensorflow-1.8.0/tensorflow/core/kernels/batch_norm_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/batch_norm_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/batch_norm_op.cc 2018-04-30 17:58:12.300340228 +0200 +@@ -72,9 +72,9 @@ + context->allocate_output(0, input.shape(), &output)); + + functor::BatchNorm()( +- context->eigen_device(), input.tensor(), mean.vec(), ++ context->eigen_device(), input.template tensor(), mean.vec(), + var.vec(), beta.vec(), gamma.vec(), variance_epsilon_, +- scale_after_normalization_, output->tensor()); ++ scale_after_normalization_, output->template tensor()); + } + + private: +@@ -148,9 +148,9 @@ + TensorShape({input.dim_size(3)}), &scratch2)); + + functor::BatchNormGrad()( +- context->eigen_device(), input.tensor(), mean.vec(), +- var.vec(), gamma.vec(), out_backprop.tensor(), +- variance_epsilon_, scale_after_normalization_, dx->tensor(), ++ context->eigen_device(), input.template tensor(), mean.vec(), ++ var.vec(), gamma.vec(), out_backprop.template tensor(), ++ variance_epsilon_, scale_after_normalization_, dx->template tensor(), + dm->vec(), dv->vec(), db->vec(), dg->vec(), + scratch1.vec(), scratch2.vec()); + } +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/batchtospace_op.cc tensorflow-1.8.0/tensorflow/core/kernels/batchtospace_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/batchtospace_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/batchtospace_op.cc 2018-04-30 17:58:12.796337214 +0200 +@@ -191,7 +191,7 @@ + output_tensor->shaped( \ + internal_output_shape.dim_sizes()), \ + internal_block_shape, internal_crops, \ +- orig_input_tensor.shaped( \ ++ orig_input_tensor.template shaped( \ + internal_input_shape.dim_sizes())))); \ + } break; \ + /**/ +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/batch_util.cc tensorflow-1.8.0/tensorflow/core/kernels/batch_util.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/batch_util.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/batch_util.cc 2018-04-30 17:58:12.392339669 +0200 +@@ -154,8 +154,8 @@ + if (element.NumElements() == 0) { + return Status::OK(); + } +- auto element_t = element.tensor(); +- auto parent_t = parent->tensor(); ++ auto element_t = element.template tensor(); ++ auto parent_t = parent->template tensor(); + Eigen::DSizes slice_indices; + slice_indices[0] = index; + Eigen::DSizes slice_size; +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/betainc_op.cc tensorflow-1.8.0/tensorflow/core/kernels/betainc_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/betainc_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/betainc_op.cc 2018-04-30 17:58:12.844336922 +0200 +@@ -91,9 +91,9 @@ + #define CASE(NDIM) \ + case NDIM: { \ + functor::Betainc functor; \ +- auto a_value = a.shaped(a_shaper.x_reshape()); \ +- auto b_value = b.shaped(b_shaper.x_reshape()); \ +- auto x_value = x.shaped(x_shaper.x_reshape()); \ ++ auto a_value = a.template shaped(a_shaper.x_reshape()); \ ++ auto b_value = b.template shaped(b_shaper.x_reshape()); \ ++ auto x_value = x.template shaped(x_shaper.x_reshape()); \ + functor.BCast(ctx->eigen_device(), a_value, \ + BCast::ToIndexArray(a_shaper.x_bcast()), b_value, \ + BCast::ToIndexArray(b_shaper.x_bcast()), x_value, \ +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/bias_op.cc tensorflow-1.8.0/tensorflow/core/kernels/bias_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/bias_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/bias_op.cc 2018-04-30 17:58:12.912336509 +0200 +@@ -136,9 +136,9 @@ + Eigen::DSizes four_dims(1, channel, 1, 1); + Eigen::DSizes broad_cast_dims(batch, 1, height, width); + const Device& d = context->eigen_device(); +- output->tensor().device(d) = +- input.tensor() + +- bias.tensor().reshape(four_dims).broadcast(broad_cast_dims); ++ output->template tensor().device(d) = ++ input.template tensor() + ++ bias.template tensor().reshape(four_dims).broadcast(broad_cast_dims); + return; + } // End of code by intel_tf. + +@@ -167,8 +167,8 @@ + void Compute(OpKernelContext* ctx, const Tensor& input, const Tensor& bias, + Tensor* output) { + functor::Bias functor; +- functor(ctx->eigen_device(), input.tensor(), bias.vec(), +- output->tensor()); ++ functor(ctx->eigen_device(), input.template tensor(), bias.vec(), ++ output->template tensor()); + } + + private: +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/boosted_trees/stats_ops.cc tensorflow-1.8.0/tensorflow/core/kernels/boosted_trees/stats_ops.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/boosted_trees/stats_ops.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/boosted_trees/stats_ops.cc 2018-04-30 17:58:13.280334272 +0200 +@@ -48,7 +48,7 @@ + std::vector::ConstTensor> stats_summary; + stats_summary.reserve(stats_summary_list.size()); + for (const auto& tensor : stats_summary_list) { +- stats_summary.emplace_back(tensor.tensor()); ++ stats_summary.emplace_back(tensor.template tensor()); + } + const Tensor* l1_t; + OP_REQUIRES_OK(context, context->input("l1", &l1_t)); +@@ -282,7 +282,7 @@ + "stats_summary", + {num_features_, max_splits_, num_buckets_, 2}, + &output_stats_summary_t)); +- auto output_stats_summary = output_stats_summary_t->tensor(); ++ auto output_stats_summary = output_stats_summary_t->template tensor(); + output_stats_summary.setZero(); + + // Partition by node, and then bucketize. +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/colorspace_op.cc tensorflow-1.8.0/tensorflow/core/kernels/colorspace_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/colorspace_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/colorspace_op.cc 2018-04-30 17:58:13.992329945 +0200 +@@ -71,7 +71,7 @@ + TensorShape({input_data.dimension(0)}), + &trange)); + +- typename TTypes::Tensor range(trange.tensor()); ++ typename TTypes::Tensor range(trange.template tensor()); + + functor::RGBToHSV()(context->eigen_device(), input_data, + range, output_data); +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/concat_op.cc tensorflow-1.8.0/tensorflow/core/kernels/concat_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/concat_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/concat_op.cc 2018-04-30 17:58:14.272328243 +0200 +@@ -135,7 +135,7 @@ + if (in.NumElements() > 0) { + int64 inputs_flat_dim1 = in.NumElements() / inputs_flat_dim0; + inputs_flat.emplace_back(new typename TTypes::ConstMatrix( +- in.shaped({inputs_flat_dim0, inputs_flat_dim1}))); ++ in.template shaped({inputs_flat_dim0, inputs_flat_dim1}))); + } + // TODO(irving): Remove check once !allow_legacy_scalars(). + output_concat_dim += in.dims() > 0 ? in.dim_size(axis) : 1; +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/conv_grad_filter_ops.cc tensorflow-1.8.0/tensorflow/core/kernels/conv_grad_filter_ops.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/conv_grad_filter_ops.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/conv_grad_filter_ops.cc 2018-04-30 17:58:14.704325618 +0200 +@@ -100,8 +100,8 @@ + Tensor* filter_backprop, TensorFormat data_format) { + const CPUDevice& d = ctx->eigen_device(); + functor::SpatialConvolutionBackwardFilter()( +- d, filter_backprop->tensor(), input.tensor(), +- out_backprop.tensor(), row_stride, col_stride, ++ d, filter_backprop->template tensor(), input.template tensor(), ++ out_backprop.template tensor(), row_stride, col_stride, + /*row_dilation=*/1, /*col_dilation=*/1); + } + }; +@@ -262,8 +262,8 @@ + + if (pad_left == pad_right && pad_top == pad_bottom) { + if (LaunchXsmmBackwardFilter()( +- context, context->eigen_device(), input.tensor(), +- filter_backprop->tensor(), out_backprop.tensor(), ++ context, context->eigen_device(), input.template tensor(), ++ filter_backprop->template tensor(), out_backprop.template tensor(), + dims.spatial_dims[0].input_size, dims.spatial_dims[1].input_size, + static_cast(dims.spatial_dims[0].stride), + static_cast(dims.spatial_dims[1].stride), +@@ -376,8 +376,8 @@ + defined TENSORFLOW_USE_LIBXSMM_BACKWARD_CONVOLUTIONS + if (pad_left == pad_right && pad_top == pad_bottom) { + if (LaunchXsmmBackwardFilter()( +- context, context->eigen_device(), input.tensor(), +- filter_backprop->tensor(), out_backprop.tensor(), ++ context, context->eigen_device(), input.template tensor(), ++ filter_backprop->template tensor(), out_backprop.template tensor(), + dims.spatial_dims[0].input_size, dims.spatial_dims[1].input_size, + static_cast(dims.spatial_dims[0].stride), + static_cast(dims.spatial_dims[1].stride), +@@ -777,9 +777,9 @@ + &compatible_input)); + + functor::PadInput()( +- ctx->template eigen_device(), To32Bit(input.tensor()), ++ ctx->template eigen_device(), To32Bit(input.template tensor()), + {{0, 0}}, {{rows_odd, cols_odd}}, +- To32Bit(compatible_input.tensor()), data_format); ++ To32Bit(compatible_input.template tensor()), data_format); + } else { + compatible_input = input; + } +@@ -844,8 +844,8 @@ + ctx->allocate_temp(DataTypeToEnum::value, nchw_shape, + &transformed_out_backprop)); + functor::NHWCToNCHW()( +- ctx->eigen_device(), out_backprop.tensor(), +- transformed_out_backprop.tensor()); ++ ctx->eigen_device(), out_backprop.template tensor(), ++ transformed_out_backprop.template tensor()); + } else { + // If depth <= 1, just reshape. + CHECK(transformed_out_backprop.CopyFrom(out_backprop, nchw_shape)); +@@ -866,8 +866,8 @@ + nchw_shape, &transformed_input)); + functor::NHWCToNCHW()( + ctx->eigen_device(), +- const_cast(compatible_input).tensor(), +- transformed_input.tensor()); ++ const_cast(compatible_input).template tensor(), ++ transformed_input.template tensor()); + } else { + // If depth <= 1, just reshape. + CHECK(transformed_input.CopyFrom(compatible_input, nchw_shape)); +@@ -978,7 +978,7 @@ + functor::ReverseTransformFilter()( + ctx->eigen_device(), + toConstTensor(pre_transformed_filter_backprop).template tensor(), +- filter_backprop->tensor()); ++ filter_backprop->template tensor()); + } + + // Forward declarations of the functor specializations for GPU. +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/conv_grad_input_ops.cc tensorflow-1.8.0/tensorflow/core/kernels/conv_grad_input_ops.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/conv_grad_input_ops.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/conv_grad_input_ops.cc 2018-04-30 17:58:14.732325447 +0200 +@@ -105,8 +105,8 @@ + Tensor* in_backprop, TensorFormat data_format) { + const CPUDevice& d = ctx->eigen_device(); + functor::SpatialConvolutionBackwardInput()( +- d, in_backprop->tensor(), filter.tensor(), +- out_backprop.tensor(), row_stride, col_stride, ++ d, in_backprop->template tensor(), filter.template tensor(), ++ out_backprop.template tensor(), row_stride, col_stride, + /*row_dilation=*/1, /*col_dilation=*/1); + } + }; +@@ -266,8 +266,8 @@ + if (pad_left == pad_right && pad_top == pad_bottom) { + if (LaunchXsmmBackwardInputConvolution()( + context, context->eigen_device(), +- in_backprop->tensor(), filter.tensor(), +- out_backprop.tensor(), dims.spatial_dims[0].input_size, ++ in_backprop->template tensor(), filter.template tensor(), ++ out_backprop.template tensor(), dims.spatial_dims[0].input_size, + dims.spatial_dims[1].input_size, + static_cast(dims.spatial_dims[0].stride), + static_cast(dims.spatial_dims[1].stride), +@@ -384,8 +384,8 @@ + if (pad_left == pad_right && pad_top == pad_bottom) { + if (LaunchXsmmBackwardInputConvolution()( + context, context->eigen_device(), +- in_backprop->tensor(), filter.tensor(), +- out_backprop.tensor(), dims.spatial_dims[0].input_size, ++ in_backprop->template tensor(), filter.template tensor(), ++ out_backprop.template tensor(), dims.spatial_dims[0].input_size, + dims.spatial_dims[1].input_size, + static_cast(dims.spatial_dims[0].stride), + static_cast(dims.spatial_dims[1].stride), +@@ -888,8 +888,8 @@ + &transformed_filter)); + + functor::TransformFilter()( +- ctx->eigen_device(), To32Bit(filter.tensor()), +- To32Bit(transformed_filter.tensor())); ++ ctx->eigen_device(), To32Bit(filter.template tensor()), ++ To32Bit(transformed_filter.template tensor())); + + Tensor transformed_out_backprop; + if (data_format == FORMAT_NHWC) { +@@ -901,8 +901,8 @@ + ctx->allocate_temp(DataTypeToEnum::value, nchw_shape, + &transformed_out_backprop)); + functor::NHWCToNCHW()( +- ctx->eigen_device(), out_backprop.tensor(), +- transformed_out_backprop.tensor()); ++ ctx->eigen_device(), out_backprop.template tensor(), ++ transformed_out_backprop.template tensor()); + } else { + // If depth <= 1, then just reshape. + CHECK(transformed_out_backprop.CopyFrom(out_backprop, nchw_shape)); +@@ -1036,9 +1036,9 @@ + functor::PadInput()( + ctx->template eigen_device(), + To32Bit(const_cast(pre_transformed_in_backprop) +- .tensor()), ++ .template tensor()), + {{0, 0}}, {{-rows_odd, -cols_odd}}, +- To32Bit(in_backprop_remove_padding.tensor()), FORMAT_NCHW); ++ To32Bit(in_backprop_remove_padding.template tensor()), FORMAT_NCHW); + + pre_transformed_in_backprop = in_backprop_remove_padding; + } +@@ -1048,7 +1048,7 @@ + functor::NCHWToNHWC()( + ctx->eigen_device(), + toConstTensor(pre_transformed_in_backprop).template tensor(), +- in_backprop->tensor()); ++ in_backprop->template tensor()); + } else { + *in_backprop = pre_transformed_in_backprop; + } +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/conv_grad_ops_3d.cc tensorflow-1.8.0/tensorflow/core/kernels/conv_grad_ops_3d.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/conv_grad_ops_3d.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/conv_grad_ops_3d.cc 2018-04-30 17:58:14.808324986 +0200 +@@ -197,8 +197,8 @@ + Eigen::DSizes eigen_strides{1, strides[0], strides[1], + strides[2], 1}; + functor::InflatePadAndShuffle()( +- context->eigen_device(), out_backprop.tensor(), +- eigen_strides, pad_dims, no_op_shuffle, padded_output.tensor()); ++ context->eigen_device(), out_backprop.template tensor(), ++ eigen_strides, pad_dims, no_op_shuffle, padded_output.template tensor()); + const Tensor& padded_output_cref = padded_output; + + // Fill a new "reverted" filter. We need to transpose the in_depth and +@@ -211,14 +211,14 @@ + Eigen::DSizes filter_order{0, 1, 2, 4, 3}; + Eigen::array filter_rev_dims{true, true, true, false, false}; + functor::ShuffleAndReverse()( +- context->eigen_device(), filter.tensor(), filter_order, +- filter_rev_dims, r_filter.tensor()); ++ context->eigen_device(), filter.template tensor(), filter_order, ++ filter_rev_dims, r_filter.template tensor()); + const Tensor& r_filter_cref = r_filter; + + // Now we can call conv_3d directly. + functor::CuboidConvolution()( +- context->eigen_device(), in_backprop->tensor(), +- padded_output_cref.tensor(), r_filter_cref.tensor(), 1, 1, ++ context->eigen_device(), in_backprop->template tensor(), ++ padded_output_cref.template tensor(), r_filter_cref.template tensor(), 1, 1, + 1, BrainPadding2EigenPadding(VALID)); + } + +@@ -319,8 +319,8 @@ + Eigen::DSizes eigen_strides{1, strides[0], strides[1], + strides[2], 1}; + functor::InflatePadAndShuffle()( +- context->eigen_device(), out_backprop.tensor(), +- eigen_strides, pad_dims, out_order, padded_output.tensor()); ++ context->eigen_device(), out_backprop.template tensor(), ++ eigen_strides, pad_dims, out_order, padded_output.template tensor()); + const Tensor& padded_output_cref = padded_output; + + // For the backprop of the filter, we need to transpose the input. +@@ -338,8 +338,8 @@ + // No need for reversing this time. + Eigen::array no_reverse{false, false, false, false, false}; + functor::ShuffleAndReverse()( +- context->eigen_device(), input.tensor(), in_order, +- no_reverse, in_shuffle.tensor()); ++ context->eigen_device(), input.template tensor(), in_order, ++ no_reverse, in_shuffle.template tensor()); + const Tensor& in_shuffle_cref = in_shuffle; + + // The output of the conv_3d would be +@@ -356,8 +356,8 @@ + context, context->allocate_temp(DataTypeToEnum::v(), + filter_shuffle_shape, &filter_shuffle)); + functor::CuboidConvolution()( +- context->eigen_device(), filter_shuffle.tensor(), +- padded_output_cref.tensor(), in_shuffle_cref.tensor(), 1, 1, ++ context->eigen_device(), filter_shuffle.template tensor(), ++ padded_output_cref.template tensor(), in_shuffle_cref.template tensor(), 1, 1, + 1, BrainPadding2EigenPadding(VALID)); + + // Now copy the filter_backprop back to the destination. +@@ -365,8 +365,8 @@ + Eigen::array filter_rev_dims{true, true, true, false, false}; + const Tensor& filter_shuffle_cref = filter_shuffle; + functor::ShuffleAndReverse()( +- context->eigen_device(), filter_shuffle_cref.tensor(), +- filter_order, filter_rev_dims, filter_backprop->tensor()); ++ context->eigen_device(), filter_shuffle_cref.template tensor(), ++ filter_order, filter_rev_dims, filter_backprop->template tensor()); + } + + private: +@@ -596,8 +596,8 @@ + filter_size[1], filter_size[2]}), + &transformed_filter)); + functor::TransformFilter()( +- context->eigen_device(), To32Bit(filter.tensor()), +- To32Bit(transformed_filter.tensor())); ++ context->eigen_device(), To32Bit(filter.template tensor()), ++ To32Bit(transformed_filter.template tensor())); + + // Shape: batch, filters, z, y, x. + Tensor transformed_out_backprop; +@@ -609,8 +609,8 @@ + DataTypeToEnum::value, nchw_shape, + &transformed_out_backprop)); + functor::NHWCToNCHW()( +- context->eigen_device(), out_backprop.tensor(), +- transformed_out_backprop.tensor()); ++ context->eigen_device(), out_backprop.template tensor(), ++ transformed_out_backprop.template tensor()); + } else { + CHECK(transformed_out_backprop.CopyFrom(out_backprop, nchw_shape)); + } +@@ -734,9 +734,9 @@ + functor::PadInput()( + context->eigen_device(), + To32Bit(const_cast(pre_transformed_in_backprop) +- .tensor()), ++ .template tensor()), + {{0, 0, 0}}, {{-planes_odd, -rows_odd, -cols_odd}}, +- To32Bit(in_backprop_remove_padding.tensor()), FORMAT_NCHW); ++ To32Bit(in_backprop_remove_padding.template tensor()), FORMAT_NCHW); + + pre_transformed_in_backprop = in_backprop_remove_padding; + } +@@ -746,7 +746,7 @@ + functor::NCHWToNHWC()( + context->eigen_device(), + toConstTensor(pre_transformed_in_backprop).template tensor(), +- in_backprop->tensor()); ++ in_backprop->template tensor()); + } else { + *in_backprop = pre_transformed_in_backprop; + } +@@ -907,9 +907,9 @@ + &compatible_input)); + functor::PadInput()( + context->template eigen_device(), +- To32Bit(input.tensor()), {{0, 0, 0}}, ++ To32Bit(input.template tensor()), {{0, 0, 0}}, + {{planes_odd, rows_odd, cols_odd}}, +- To32Bit(compatible_input.tensor()), data_format_); ++ To32Bit(compatible_input.template tensor()), data_format_); + } else { + compatible_input = input; + } +@@ -965,8 +965,8 @@ + &transformed_out_backprop)); + if (out_depth > 1) { + functor::NHWCToNCHW()( +- context->eigen_device(), out_backprop.tensor(), +- transformed_out_backprop.tensor()); ++ context->eigen_device(), out_backprop.template tensor(), ++ transformed_out_backprop.template tensor()); + } else { + CHECK(transformed_out_backprop.CopyFrom(out_backprop, nchw_shape)); + } +@@ -984,8 +984,8 @@ + nchw_shape, &transformed_input)); + functor::NHWCToNCHW()( + context->eigen_device(), +- const_cast(compatible_input).tensor(), +- transformed_input.tensor()); ++ const_cast(compatible_input).template tensor(), ++ transformed_input.template tensor()); + } else { + CHECK(transformed_input.CopyFrom(compatible_input, nchw_shape)); + } +@@ -1094,7 +1094,7 @@ + functor::ReverseTransformFilter()( + context->eigen_device(), + toConstTensor(pre_transformed_filter_backprop).template tensor(), +- filter_backprop->tensor()); ++ filter_backprop->template tensor()); + } + + private: +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/conv_ops_3d.cc tensorflow-1.8.0/tensorflow/core/kernels/conv_ops_3d.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/conv_ops_3d.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/conv_ops_3d.cc 2018-04-30 17:58:14.856324694 +0200 +@@ -56,8 +56,8 @@ + "currently only supports the NHWC " + "tensor format.")); + functor::CuboidConvolution()( +- context->eigen_device(), output->tensor(), +- input.tensor(), filter.tensor(), strides[2], strides[1], ++ context->eigen_device(), output->template tensor(), ++ input.template tensor(), filter.template tensor(), strides[2], strides[1], + strides[0], BrainPadding2EigenPadding(padding)); + } + }; +@@ -276,9 +276,9 @@ + &transformed_input)); + + functor::PadInput()( +- ctx->eigen_device(), To32Bit(input_param.tensor()), ++ ctx->eigen_device(), To32Bit(input_param.template tensor()), + {{0, 0, 0}}, {{planes_odd, rows_odd, cols_odd}}, +- To32Bit(transformed_input.tensor()), data_format); ++ To32Bit(transformed_input.template tensor()), data_format); + input = transformed_input; + in_rows = new_in_rows; + in_cols = new_in_cols; +@@ -298,8 +298,8 @@ + // NCDHW is the only format universally supported by cuDNN. + functor::NHWCToNCHW()( + ctx->eigen_device(), +- const_cast(input).tensor(), +- transformed_input.tensor()); ++ const_cast(input).template tensor(), ++ transformed_input.template tensor()); + input = transformed_input; + } else { + CHECK(input.CopyFrom(input, nchw_shape)); +@@ -346,8 +346,8 @@ + // filter: [x, y, z, in, out] + // t_filter: [out, in, x, y, z] + functor::TransformFilter()( +- ctx->eigen_device(), To32Bit(filter.tensor()), +- To32Bit(transformed_filter.tensor())); ++ ctx->eigen_device(), To32Bit(filter.template tensor()), ++ To32Bit(transformed_filter.template tensor())); + + Tensor transformed_output; + OP_REQUIRES_OK( +@@ -458,8 +458,8 @@ + // output: [b, x, y, z, out] + functor::NCHWToNHWC()( + ctx->eigen_device(), +- const_cast(transformed_output).tensor(), +- output->tensor()); ++ const_cast(transformed_output).template tensor(), ++ output->template tensor()); + } else { + *output = transformed_output; + } +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/conv_ops.cc tensorflow-1.8.0/tensorflow/core/kernels/conv_ops.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/conv_ops.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/conv_ops.cc 2018-04-30 17:58:14.676325788 +0200 +@@ -82,8 +82,8 @@ + functor::MatMulConvFunctor()( + ctx->eigen_device(), + output->shaped({conv_width, filter.dim_size(3)}), +- input.shaped({conv_width, filter.dim_size(2)}), +- filter.shaped({filter.dim_size(2), filter.dim_size(3)}), ++ input.template shaped({conv_width, filter.dim_size(2)}), ++ filter.template shaped({filter.dim_size(2), filter.dim_size(3)}), + dim_pair); + } else if (filter.dim_size(0) == input.dim_size(1) && + filter.dim_size(1) == input.dim_size(2) && row_dilation == 1 && +@@ -98,12 +98,12 @@ + functor::MatMulConvFunctor()( + ctx->eigen_device(), + output->shaped({input.dim_size(0), filter.dim_size(3)}), +- input.shaped({input.dim_size(0), k}), +- filter.shaped({k, filter.dim_size(3)}), dim_pair); ++ input.template shaped({input.dim_size(0), k}), ++ filter.template shaped({k, filter.dim_size(3)}), dim_pair); + } else { + functor::SpatialConvolution()( +- ctx->eigen_device(), output->tensor(), +- input.tensor(), filter.tensor(), row_stride, col_stride, ++ ctx->eigen_device(), output->template tensor(), ++ input.template tensor(), filter.template tensor(), row_stride, col_stride, + row_dilation, col_dilation, BrainPadding2EigenPadding(padding)); + } + } +@@ -597,9 +597,9 @@ + &transformed_input)); + + functor::PadInput()( +- ctx->eigen_device(), To32Bit(input_param.tensor()), ++ ctx->eigen_device(), To32Bit(input_param.template tensor()), + {{0, 0}}, {{rows_odd, cols_odd}}, +- To32Bit(transformed_input.tensor()), data_format); ++ To32Bit(transformed_input.template tensor()), data_format); + + input = transformed_input; + in_rows = new_in_rows; +@@ -617,8 +617,8 @@ + nchw_shape, &transformed_input)); + functor::NHWCToNCHW()( + ctx->eigen_device(), +- const_cast(input).tensor(), +- transformed_input.tensor()); ++ const_cast(input).template tensor(), ++ transformed_input.template tensor()); + input = transformed_input; + } else { + // If depth <= 1, then just reshape. +@@ -662,8 +662,8 @@ + &transformed_filter)); + + functor::TransformFilter()( +- ctx->eigen_device(), To32Bit(filter.tensor()), +- To32Bit(transformed_filter.tensor())); ++ ctx->eigen_device(), To32Bit(filter.template tensor()), ++ To32Bit(transformed_filter.template tensor())); + + Tensor transformed_output; + OP_REQUIRES_OK( +@@ -773,8 +773,8 @@ + if (data_format == FORMAT_NHWC) { + functor::NCHWToNHWC()( + ctx->eigen_device(), +- const_cast(transformed_output).tensor(), +- output->tensor()); ++ const_cast(transformed_output).template tensor(), ++ output->template tensor()); + } else { + *output = transformed_output; + } +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/crop_and_resize_op.cc tensorflow-1.8.0/tensorflow/core/kernels/crop_and_resize_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/crop_and_resize_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/crop_and_resize_op.cc 2018-04-30 17:58:15.056323478 +0200 +@@ -178,16 +178,16 @@ + const Tensor& boxes = context->input(1); + const Tensor& box_index = context->input(2); + const bool status = functor::CropAndResize()( +- context, image.tensor(), boxes.tensor(), +- box_index.tensor(), extrapolation_value_, +- output->tensor()); ++ context, image.template tensor(), boxes.template tensor(), ++ box_index.template tensor(), extrapolation_value_, ++ output->template tensor()); + if (!status) { + context->SetStatus( + errors::Internal("Failed launch CropAndResizeKernel.")); + } + }; + +- RunIfBoxIndexIsValid(context, box_index.tensor(), ++ RunIfBoxIndexIsValid(context, box_index.template tensor(), + batch_size, std::move(compute_callback), + std::move(done)); + } +@@ -378,16 +378,16 @@ + const Tensor& boxes = context->input(1); + const Tensor& box_index = context->input(2); + const bool status = functor::CropAndResizeBackpropImage()( +- context->eigen_device(), grads.tensor(), +- boxes.tensor(), box_index.tensor(), +- output->tensor()); ++ context->eigen_device(), grads.template tensor(), ++ boxes.template tensor(), box_index.template tensor(), ++ output->template tensor()); + if (!status) { + context->SetStatus(errors::Internal( + "Failed launch CropAndResizeBackpropImage kernel.")); + } + }; + +- RunIfBoxIndexIsValid(context, box_index.tensor(), ++ RunIfBoxIndexIsValid(context, box_index.template tensor(), + batch_size, std::move(compute_callback), + std::move(done)); + } +@@ -543,16 +543,16 @@ + const Tensor& boxes = context->input(2); + const Tensor& box_index = context->input(3); + const bool status = functor::CropAndResizeBackpropBoxes()( +- context->eigen_device(), grads.tensor(), +- image.tensor(), boxes.tensor(), +- box_index.tensor(), output->tensor()); ++ context->eigen_device(), grads.template tensor(), ++ image.template tensor(), boxes.template tensor(), ++ box_index.template tensor(), output->template tensor()); + if (!status) { + context->SetStatus(errors::Internal( + "Failed launch CropAndResizeBackpropBoxes kernel.")); + } + }; + +- RunIfBoxIndexIsValid(context, box_index.tensor(), ++ RunIfBoxIndexIsValid(context, box_index.template tensor(), + batch_size, std::move(compute_callback), + std::move(done)); + } +@@ -732,7 +732,7 @@ + &isvalid_dev_tensor), + done); + typename TTypes::Tensor isvalid_dev = +- isvalid_dev_tensor.tensor(); ++ isvalid_dev_tensor.template tensor(); + + // Run the actual box check on the device. + functor::CheckValidBoxIndexHelper()( +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/ctc_decoder_ops.cc tensorflow-1.8.0/tensorflow/core/kernels/ctc_decoder_ops.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/ctc_decoder_ops.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/ctc_decoder_ops.cc 2018-04-30 17:58:15.244322336 +0200 +@@ -197,7 +197,7 @@ + errors::InvalidArgument("num_classes cannot exceed max int")); + const int num_classes = static_cast(num_classes_raw); + +- auto inputs_t = inputs->tensor(); ++ auto inputs_t = inputs->template tensor(); + + for (std::size_t t = 0; t < max_time; ++t) { + input_list_t.emplace_back(inputs_t.data() + t * batch_size * num_classes, +@@ -265,7 +265,7 @@ + ctx, &inputs, &seq_len, &log_prob, &decoded_indices, + &decoded_values, &decoded_shape)); + +- auto inputs_t = inputs->tensor(); ++ auto inputs_t = inputs->template tensor(); + auto seq_len_t = seq_len->vec(); + auto log_prob_t = log_prob->matrix(); + +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/ctc_loss_op.cc tensorflow-1.8.0/tensorflow/core/kernels/ctc_loss_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/ctc_loss_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/ctc_loss_op.cc 2018-04-30 17:58:15.268322190 +0200 +@@ -140,8 +140,8 @@ + Tensor* gradient; + OP_REQUIRES_OK(ctx, + ctx->allocate_output("gradient", inputs_shape, &gradient)); +- auto gradient_t = gradient->tensor(); +- auto inputs_t = inputs->tensor(); ++ auto gradient_t = gradient->template tensor(); ++ auto inputs_t = inputs->template tensor(); + std::vector gradient_list_t; + std::vector input_list_t; + +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/cudnn_pooling_gpu.cc tensorflow-1.8.0/tensorflow/core/kernels/cudnn_pooling_gpu.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/cudnn_pooling_gpu.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/cudnn_pooling_gpu.cc 2018-04-30 17:58:15.388321461 +0200 +@@ -51,8 +51,8 @@ + data_format), + &transformed_input)); + functor::NHWCToNCHW()(context->eigen_device(), +- tensor_in.tensor(), +- transformed_input.tensor()); ++ tensor_in.template tensor(), ++ transformed_input.template tensor()); + } else { + transformed_input = tensor_in; + } +@@ -109,7 +109,7 @@ + functor::NCHWToNHWC()( + context->eigen_device(), + toConstTensor(transformed_output).template tensor(), +- output->tensor()); ++ output->template tensor()); + } + } + +@@ -173,17 +173,17 @@ + if (data_format == FORMAT_NHWC) { + if (tensor_in != nullptr) { + functor::NHWCToNCHW()(context->eigen_device(), +- tensor_in->tensor(), +- transformed_input.tensor()); ++ tensor_in->template tensor(), ++ transformed_input.template tensor()); + } + if (tensor_out != nullptr) { + functor::NHWCToNCHW()(context->eigen_device(), +- tensor_out->tensor(), +- transformed_output.tensor()); ++ tensor_out->template tensor(), ++ transformed_output.template tensor()); + } + functor::NHWCToNCHW()( +- context->eigen_device(), out_backprop.tensor(), +- transformed_output_backprop.tensor()); ++ context->eigen_device(), out_backprop.template tensor(), ++ transformed_output_backprop.template tensor()); + } + + perftools::gputools::dnn::PoolingDescriptor pooling_desc(3); +@@ -239,7 +239,7 @@ + functor::NCHWToNHWC()( + context->eigen_device(), + toConstTensor(transformed_input_backprop).template tensor(), +- input_backprop->tensor()); ++ input_backprop->template tensor()); + } + } + +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/depthtospace_op.cc tensorflow-1.8.0/tensorflow/core/kernels/depthtospace_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/depthtospace_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/depthtospace_op.cc 2018-04-30 17:58:20.716289083 +0200 +@@ -109,8 +109,8 @@ + ShapeFromFormat(data_format_, batch_size, output_height, + output_width, output_depth), + &outputs_tensor)); +- auto Tinput = input.tensor(); +- auto Toutput = outputs_tensor->tensor(); ++ auto Tinput = input.template tensor(); ++ auto Toutput = outputs_tensor->template tensor(); + + if (std::is_same::value) { + if (is_int8x4) { +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/dilation_ops.cc tensorflow-1.8.0/tensorflow/core/kernels/dilation_ops.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/dilation_ops.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/dilation_ops.cc 2018-04-30 17:58:21.108286701 +0200 +@@ -147,9 +147,9 @@ + } + + functor::Dilation()( +- context->eigen_device(), input.tensor(), +- filter.tensor(), stride_rows, stride_cols, rate_rows, rate_cols, +- pad_top, pad_left, output->tensor()); ++ context->eigen_device(), input.template tensor(), ++ filter.template tensor(), stride_rows, stride_cols, rate_rows, rate_cols, ++ pad_top, pad_left, output->template tensor()); + } + + std::vector strides_; +@@ -253,10 +253,10 @@ + } + + functor::DilationBackpropInput()( +- context->eigen_device(), input.tensor(), +- filter.tensor(), out_backprop.tensor(), stride_rows, ++ context->eigen_device(), input.template tensor(), ++ filter.template tensor(), out_backprop.template tensor(), stride_rows, + stride_cols, rate_rows, rate_cols, pad_top, pad_left, +- in_backprop->tensor()); ++ in_backprop->template tensor()); + } + + std::vector strides_; +@@ -373,10 +373,10 @@ + } + + functor::DilationBackpropFilter()( +- context->eigen_device(), input.tensor(), +- filter.tensor(), out_backprop.tensor(), stride_rows, ++ context->eigen_device(), input.template tensor(), ++ filter.template tensor(), out_backprop.template tensor(), stride_rows, + stride_cols, rate_rows, rate_cols, pad_top, pad_left, +- filter_backprop->tensor()); ++ filter_backprop->template tensor()); + } + + std::vector strides_; +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/draw_bounding_box_op.cc tensorflow-1.8.0/tensorflow/core/kernels/draw_bounding_box_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/draw_bounding_box_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/draw_bounding_box_op.cc 2018-04-30 17:58:21.176286287 +0200 +@@ -83,12 +83,12 @@ + context->allocate_output( + 0, TensorShape({batch_size, height, width, depth}), &output)); + +- output->tensor() = images.tensor(); +- auto canvas = output->tensor(); ++ output->template tensor() = images.template tensor(); ++ auto canvas = output->template tensor(); + + for (int64 b = 0; b < batch_size; ++b) { + const int64 num_boxes = boxes.dim_size(1); +- const auto tboxes = boxes.tensor(); ++ const auto tboxes = boxes.template tensor(); + for (int64 bb = 0; bb < num_boxes; ++bb) { + int64 color_index = bb % color_table_length; + const int64 min_box_row = +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/dynamic_stitch_op.cc tensorflow-1.8.0/tensorflow/core/kernels/dynamic_stitch_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/dynamic_stitch_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/dynamic_stitch_op.cc 2018-04-30 17:58:21.272285704 +0200 +@@ -244,7 +244,7 @@ + auto indices_vec = indices.flat(); + const Tensor& data = data_inputs[input_num]; + auto data_flat = +- data.shaped({indices_vec.dimension(0), slice_size}); ++ data.template shaped({indices_vec.dimension(0), slice_size}); + + if (DataTypeCanUseMemcpy(DataTypeToEnum::v())) { + T* merged_base = &merged_flat(0, 0); +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/extract_image_patches_op.cc tensorflow-1.8.0/tensorflow/core/kernels/extract_image_patches_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/extract_image_patches_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/extract_image_patches_op.cc 2018-04-30 17:58:21.912281815 +0200 +@@ -105,9 +105,9 @@ + } + + functor::ExtractImagePatchesForward()( +- context->eigen_device(), input.tensor(), ksize_rows, ++ context->eigen_device(), input.template tensor(), ksize_rows, + ksize_cols, stride_rows, stride_cols, rate_rows, rate_cols, +- BrainPadding2EigenPadding(padding_), output->tensor()); ++ BrainPadding2EigenPadding(padding_), output->template tensor()); + } + + private: +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/extract_jpeg_shape_op.cc tensorflow-1.8.0/tensorflow/core/kernels/extract_jpeg_shape_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/extract_jpeg_shape_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/extract_jpeg_shape_op.cc 2018-04-30 17:58:21.980281402 +0200 +@@ -57,7 +57,7 @@ + Tensor* image_shape = nullptr; + OP_REQUIRES_OK(context, + context->allocate_output(0, TensorShape({3}), &image_shape)); +- auto image_shape_data = image_shape->tensor(); ++ auto image_shape_data = image_shape->template tensor(); + image_shape_data(0) = height; + image_shape_data(1) = width; + image_shape_data(2) = components; +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/fused_batch_norm_op.cc tensorflow-1.8.0/tensorflow/core/kernels/fused_batch_norm_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/fused_batch_norm_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/fused_batch_norm_op.cc 2018-04-30 17:58:22.516278145 +0200 +@@ -58,13 +58,13 @@ + OP_REQUIRES(context, tensor_format == FORMAT_NHWC, + errors::Internal("The CPU implementation of FusedBatchNorm " + "only supports NHWC tensor format for now.")); +- typename TTypes::ConstTensor x(x_input.tensor()); ++ typename TTypes::ConstTensor x(x_input.template tensor()); + typename TTypes::ConstVec scale(scale_input.vec()); + typename TTypes::ConstVec offset(offset_input.vec()); + typename TTypes::ConstVec estimated_mean(estimated_mean_input.vec()); + typename TTypes::ConstVec estimated_variance( + estimated_variance_input.vec()); +- typename TTypes::Tensor y(y_output->tensor()); ++ typename TTypes::Tensor y(y_output->template tensor()); + typename TTypes::Vec batch_mean(batch_mean_output->vec()); + typename TTypes::Vec batch_var(batch_var_output->vec()); + typename TTypes::Vec saved_mean(saved_mean_output->vec()); +@@ -141,12 +141,12 @@ + errors::Internal("The CPU implementation of FusedBatchNormGrad " + "only supports NHWC tensor format for now.")); + typename TTypes::ConstTensor y_backprop( +- y_backprop_input.tensor()); +- typename TTypes::ConstTensor x(x_input.tensor()); ++ y_backprop_input.template tensor()); ++ typename TTypes::ConstTensor x(x_input.template tensor()); + typename TTypes::ConstVec scale(scale_input.vec()); + typename TTypes::ConstVec mean(mean_input.vec()); + typename TTypes::ConstVec variance(variance_input.vec()); +- typename TTypes::Tensor x_backprop(x_backprop_output->tensor()); ++ typename TTypes::Tensor x_backprop(x_backprop_output->template tensor()); + typename TTypes::Vec scale_backprop(scale_backprop_output->vec()); + typename TTypes::Vec offset_backprop(offset_backprop_output->vec()); + +@@ -263,8 +263,8 @@ + &x_transformed)); + functor::NHWCToNCHW()( + context->eigen_device(), +- const_cast(x_maybe_transformed).tensor(), +- x_transformed.tensor()); ++ const_cast(x_maybe_transformed).template tensor(), ++ x_transformed.template tensor()); + x_maybe_transformed = x_transformed; + + OP_REQUIRES_OK(context, context->allocate_temp( +@@ -353,8 +353,8 @@ + if (tensor_format == FORMAT_NHWC) { + functor::NCHWToNHWC()( + context->eigen_device(), +- const_cast(y_transformed).tensor(), +- y->tensor()); ++ const_cast(y_transformed).template tensor(), ++ y->template tensor()); + } + } + }; +@@ -404,8 +404,8 @@ + functor::NHWCToNCHW()( + context->eigen_device(), + const_cast(y_backprop_maybe_transformed) +- .tensor(), +- y_backprop_transformed.tensor()); ++ .template tensor(), ++ y_backprop_transformed.template tensor()); + y_backprop_maybe_transformed = y_backprop_transformed; + + OP_REQUIRES_OK(context, context->allocate_temp( +@@ -415,8 +415,8 @@ + &x_transformed)); + functor::NHWCToNCHW()( + context->eigen_device(), +- const_cast(x_maybe_transformed).tensor(), +- x_transformed.tensor()); ++ const_cast(x_maybe_transformed).template tensor(), ++ x_transformed.template tensor()); + x_maybe_transformed = x_transformed; + + // Allocate memory for transformed outputs in 'NCHW' +@@ -476,8 +476,8 @@ + if (tensor_format == FORMAT_NHWC) { + functor::NCHWToNHWC()( + context->eigen_device(), +- const_cast(x_backprop_transformed).tensor(), +- x_backprop->tensor()); ++ const_cast(x_backprop_transformed).template tensor(), ++ x_backprop->template tensor()); + } + } + }; +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/fused_batch_norm_op.h tensorflow-1.8.0/tensorflow/core/kernels/fused_batch_norm_op.h +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/fused_batch_norm_op.h 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/fused_batch_norm_op.h 2018-04-30 17:58:22.560277878 +0200 +@@ -70,12 +70,12 @@ + typename TTypes::Vec scratch1, + typename TTypes::Vec scratch2) { + typename TTypes::ConstTensor y_backprop( +- y_backprop_input.tensor()); +- typename TTypes::ConstTensor input(x_input.tensor()); ++ y_backprop_input.template tensor()); ++ typename TTypes::ConstTensor input(x_input.template tensor()); + typename TTypes::ConstVec scale(scale_input.vec()); + typename TTypes::ConstVec pop_mean(pop_mean_input.vec()); + typename TTypes::ConstVec pop_var(pop_variance_input.vec()); +- typename TTypes::Tensor x_backprop(x_backprop_output->tensor()); ++ typename TTypes::Tensor x_backprop(x_backprop_output->template tensor()); + typename TTypes::Vec scale_backprop(scale_backprop_output->vec()); + typename TTypes::Vec offset_backprop(offset_backprop_output->vec()); + +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/gather_op.cc tensorflow-1.8.0/tensorflow/core/kernels/gather_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/gather_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/gather_op.cc 2018-04-30 17:58:23.336273163 +0200 +@@ -103,7 +103,7 @@ + OP_REQUIRES_OK(c, c->allocate_output(0, result_shape, &out)); + if (N > 0 && outer_size > 0 && inner_size > 0) { + auto params_flat = +- params.shaped({outer_size, gather_dim_size, inner_size}); ++ params.template shaped({outer_size, gather_dim_size, inner_size}); + auto indices_flat = indices.flat(); + auto out_flat = out->shaped({outer_size, N, inner_size}); + +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/inplace_ops.cc tensorflow-1.8.0/tensorflow/core/kernels/inplace_ops.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/inplace_ops.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/inplace_ops.cc 2018-04-30 17:58:24.476266236 +0200 +@@ -34,7 +34,7 @@ + template + Status DoParallelConcatUpdate(const Device& d, const Tensor& value, int32 loc, + Tensor* output) { +- auto Tvalue = value.shaped({1, value.NumElements()}); ++ auto Tvalue = value.template shaped({1, value.NumElements()}); + auto Toutput = output->flat_outer_dims(); + auto nrows = Toutput.dimension(0); + auto r = (loc % nrows + nrows) % nrows; // Guard index range. +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/list_kernels.h tensorflow-1.8.0/tensorflow/core/kernels/list_kernels.h +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/list_kernels.h 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/list_kernels.h 2018-04-30 17:58:24.708264826 +0200 +@@ -113,7 +113,7 @@ + l->element_shape.DebugString(), + " and tensor shape: ", t.shape().DebugString())); + inputs_flat.emplace_back(new typename TTypes::ConstMatrix( +- t.shaped({1, t.NumElements()}))); ++ t.template shaped({1, t.NumElements()}))); + } + auto output_flat = output->shaped({1, output->NumElements()}); + +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/lookup_table_op.cc tensorflow-1.8.0/tensorflow/core/kernels/lookup_table_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/lookup_table_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/lookup_table_op.cc 2018-04-30 17:58:24.920263538 +0200 +@@ -351,7 +351,7 @@ + expected_shape.DebugString(), " got ", + key.shape().DebugString()); + } +- const auto key_matrix = key.shaped({num_elements, key_size}); ++ const auto key_matrix = key.template shaped({num_elements, key_size}); + auto value_matrix = value->shaped({num_elements, value_size}); + const auto default_flat = default_value.flat(); + +@@ -503,8 +503,8 @@ + const int64 num_elements = key.dim_size(0); + const int64 value_size = value_shape_.num_elements(); + const int64 key_size = key_shape_.num_elements(); +- const auto key_matrix = key.shaped({num_elements, key_size}); +- auto value_matrix = value.shaped({num_elements, value_size}); ++ const auto key_matrix = key.template shaped({num_elements, key_size}); ++ auto value_matrix = value.template shaped({num_elements, value_size}); + + auto key_buckets_matrix = + key_buckets_.AccessTensor(ctx)->template matrix(); +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/lrn_op.cc tensorflow-1.8.0/tensorflow/core/kernels/lrn_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/lrn_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/lrn_op.cc 2018-04-30 17:58:25.064262664 +0200 +@@ -90,7 +90,7 @@ + return; + } + +- auto in_shaped = in.shaped({nodes * batch, depth}); ++ auto in_shaped = in.template shaped({nodes * batch, depth}); + + // Multiplying the input with the band matrix has the effect of reducing the + // correct patch along the depth. +@@ -318,9 +318,9 @@ + const int64 cols = in_grads.dim_size(2); + const int64 depth = in_grads.dim_size(3); + const auto nodes = cols * rows; +- auto grads_shaped = in_grads.shaped({nodes * batch, depth}); +- auto in_shaped = in_image.shaped({nodes * batch, depth}); +- auto activations = out_image.shaped({nodes * batch, depth}); ++ auto grads_shaped = in_grads.template shaped({nodes * batch, depth}); ++ auto in_shaped = in_image.template shaped({nodes * batch, depth}); ++ auto activations = out_image.template shaped({nodes * batch, depth}); + + auto out_shaped = output->shaped({nodes * batch, depth}); + out_shaped.setZero(); +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/lrn_op_test.cc tensorflow-1.8.0/tensorflow/core/kernels/lrn_op_test.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/lrn_op_test.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/lrn_op_test.cc 2018-04-30 17:58:25.084262542 +0200 +@@ -65,7 +65,7 @@ + Eigen::Tensor expected(batch_size, rows, cols, + depth); + auto out = expected.reshape(Eigen::DSizes{rest, depth}); +- auto in = input.shaped({rest, depth}); ++ auto in = input.template shaped({rest, depth}); + + for (int64 i = 0; i < rest; ++i) { + Eigen::Tensor out_col(depth); +@@ -80,7 +80,7 @@ + } + out.chip<0>(i) = out_col; + } +- auto actual = GetOutput(0)->tensor(); ++ auto actual = GetOutput(0)->template tensor(); + Eigen::Tensor sum = + ((expected - actual).abs() > actual.constant(tol_)) + .select(actual.constant(1), actual.constant(0)) +@@ -104,7 +104,7 @@ + AddInput(TensorShape({1, 1, 1, 96}), + [this](int i) -> float { return i + 1; }); + TF_ASSERT_OK(RunOpKernel()); +- auto actual = GetOutput(0)->tensor(); ++ auto actual = GetOutput(0)->template tensor(); + + // Output for Node 0 with Value 1: + // 1 / (1 + 0.1*(1^2 + 2^2 + 3^2 + 4^2 + 5^2 + 6^2))^2 +@@ -140,7 +140,7 @@ + AddInput(TensorShape({1, 1, 1, 16}), + [this](int i) -> float { return i + 1; }); + TF_ASSERT_OK(RunOpKernel()); +- auto actual = GetOutput(0)->tensor(); ++ auto actual = GetOutput(0)->template tensor(); + + // Output for Node 0 with Value 1: + // 1 / (1 + 0.1*(1^2 + 2^2 + 3^2 + 4^2 + 5^2 + 6^2))^2 +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/mirror_pad_op.cc tensorflow-1.8.0/tensorflow/core/kernels/mirror_pad_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/mirror_pad_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/mirror_pad_op.cc 2018-04-30 17:58:26.092256417 +0200 +@@ -122,8 +122,8 @@ + #define MIRROR_PAD_CASE(i) \ + case i: { \ + functor::MirrorPad()( \ +- context->eigen_device(), To32Bit(output->tensor()), \ +- To32Bit(in0.tensor()), paddings, offset_); \ ++ context->eigen_device(), To32Bit(output->template tensor()), \ ++ To32Bit(in0.template tensor()), paddings, offset_); \ + break; \ + } + +@@ -333,9 +333,9 @@ + #define MIRROR_PAD_GRAD_CASE(k) \ + case k: { \ + functor::MirrorPadGrad()( \ +- context->eigen_device(), To32Bit(output->tensor()), \ +- To32Bit(in0.tensor()), paddings, offset_, \ +- To32Bit(scratch.tensor())); \ ++ context->eigen_device(), To32Bit(output->template tensor()), \ ++ To32Bit(in0.template tensor()), paddings, offset_, \ ++ To32Bit(scratch.template tensor())); \ + break; \ + } + +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/mkl_concat_op.cc tensorflow-1.8.0/tensorflow/core/kernels/mkl_concat_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/mkl_concat_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/mkl_concat_op.cc 2018-04-30 17:58:26.376254692 +0200 +@@ -127,7 +127,7 @@ + if (in.NumElements() > 0) { + int64 inputs_flat_dim1 = in.NumElements() / inputs_flat_dim0; + inputs_flat.emplace_back(new typename TTypes::ConstMatrix( +- in.shaped({inputs_flat_dim0, inputs_flat_dim1}))); ++ in.template shaped({inputs_flat_dim0, inputs_flat_dim1}))); + } + // TODO(irving): Remove check once !allow_legacy_scalars(). + output_concat_dim += in.dims() > 0 ? in.dim_size(axis) : 1; +@@ -206,7 +206,7 @@ + if (in.NumElements() > 0) { + int64 inputs_flat_dim1 = in.NumElements() / inputs_flat_dim0; + inputs_flat.emplace_back(new typename TTypes::ConstMatrix( +- in.shaped({inputs_flat_dim0, inputs_flat_dim1}))); ++ in.template shaped({inputs_flat_dim0, inputs_flat_dim1}))); + } + output_concat_dim += + input_shapes[i].dims() > 0 ? input_shapes[i].dim_size(axis) : 1; +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/mkl_lrn_op.cc tensorflow-1.8.0/tensorflow/core/kernels/mkl_lrn_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/mkl_lrn_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/mkl_lrn_op.cc 2018-04-30 17:58:26.636253112 +0200 +@@ -290,7 +290,7 @@ + const int depth = static_cast(input.dim_size(3)); + const int nodes = cols * rows; + +- auto in_shaped = input.shaped({nodes * batch, depth}); ++ auto in_shaped = input.template shaped({nodes * batch, depth}); + // Multiplying the input with the band matrix has the effect of reducing + // the + // correct patch along the depth. +@@ -660,10 +660,10 @@ + const int64 depth = static_cast(in_grads.dim_size(3)); + const auto nodes = cols * rows; + +- auto grads_shaped = in_grads.shaped({nodes * batch, depth}); ++ auto grads_shaped = in_grads.template shaped({nodes * batch, depth}); + +- auto in_shaped = in_image.shaped({nodes * batch, depth}); +- auto activations = out_image.shaped({nodes * batch, depth}); ++ auto in_shaped = in_image.template shaped({nodes * batch, depth}); ++ auto activations = out_image.template shaped({nodes * batch, depth}); + + Tensor* output; + MklShape mkl_output_mkl_shape; +@@ -897,7 +897,7 @@ + const int depth = static_cast(input.dim_size(3)); + const int nodes = cols * rows; + +- auto in_shaped = input.shaped({nodes * batch, depth}); ++ auto in_shaped = input.template shaped({nodes * batch, depth}); + // Multiplying the input with the band matrix has the effect of reducing + // the + // correct patch along the depth. +@@ -1230,10 +1230,10 @@ + const auto nodes = cols * rows; + + auto grads_shaped = +- input_gradient_tensor.shaped({nodes * batch, depth}); ++ input_gradient_tensor.template shaped({nodes * batch, depth}); + +- auto in_shaped = orig_input_tensor.shaped({nodes * batch, depth}); +- auto activations = orig_output_tensor.shaped({nodes * batch, depth}); ++ auto in_shaped = orig_input_tensor.template shaped({nodes * batch, depth}); ++ auto activations = orig_output_tensor.template shaped({nodes * batch, depth}); + + Tensor* output_dnn_data; + MklShape mkl_output_mkl_shape; +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/mkl_transpose_op.cc tensorflow-1.8.0/tensorflow/core/kernels/mkl_transpose_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/mkl_transpose_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/mkl_transpose_op.cc 2018-04-30 17:58:26.852251800 +0200 +@@ -31,8 +31,8 @@ + // Specifically, the returned tensor output meets the following condition: + // 1) output.dims() == input.dims(); + // 2) output.dim_size(i) == input.dim_size(perm[i]); +-// 3) output.tensor(i_0, i_1, ..., i_N-1) == +-// input.tensor(j_0, j_1, ..., j_N-1), ++// 3) output.template tensor(i_0, i_1, ..., i_N-1) == ++// input.template tensor(j_0, j_1, ..., j_N-1), + // where i_s == j_{perm[s]} + // + // REQUIRES: perm is a vector of int32. +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/non_max_suppression_op.cc tensorflow-1.8.0/tensorflow/core/kernels/non_max_suppression_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/non_max_suppression_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/non_max_suppression_op.cc 2018-04-30 17:58:27.068250487 +0200 +@@ -105,7 +105,7 @@ + } + + const int output_size = std::min(max_output_size.scalar()(), num_boxes); +- TTypes::ConstTensor boxes_data = boxes.tensor(); ++ TTypes::ConstTensor boxes_data = boxes.template tensor(); + + std::vector scores_data(num_boxes); + std::copy_n(scores.flat().data(), num_boxes, scores_data.begin()); +@@ -138,7 +138,7 @@ + Tensor* output = nullptr; + TensorShape output_shape({static_cast(selected.size())}); + OP_REQUIRES_OK(context, context->allocate_output(0, output_shape, &output)); +- TTypes::Tensor selected_indices_data = output->tensor(); ++ TTypes::Tensor selected_indices_data = output->template tensor(); + std::copy_n(selected.begin(), selected.size(), selected_indices_data.data()); + } + +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/one_hot_op.cc tensorflow-1.8.0/tensorflow/core/kernels/one_hot_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/one_hot_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/one_hot_op.cc 2018-04-30 17:58:27.184249783 +0200 +@@ -107,7 +107,7 @@ + + // Split indices into matrix of size prefix_dim_size x suffix_dim_size + auto indices_t = +- indices.shaped({prefix_dim_size, suffix_dim_size}); ++ indices.template shaped({prefix_dim_size, suffix_dim_size}); + // Split output into 3-Tensor of size: + // prefix_dim_size x depth x suffix_dim_size. + auto output_t = +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/pack_op.cc tensorflow-1.8.0/tensorflow/core/kernels/pack_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/pack_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/pack_op.cc 2018-04-30 17:58:27.392248519 +0200 +@@ -110,7 +110,7 @@ + inputs_flat.reserve(num); + for (int i = 0; i < num; ++i) { + inputs_flat.emplace_back(new typename TTypes::ConstMatrix( +- values[i].shaped({before_dim, after_dim}))); ++ values[i].template shaped({before_dim, after_dim}))); + } + #if GOOGLE_CUDA + if (std::is_same::value) { +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/padding_fifo_queue.cc tensorflow-1.8.0/tensorflow/core/kernels/padding_fifo_queue.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/padding_fifo_queue.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/padding_fifo_queue.cc 2018-04-30 17:58:27.488247936 +0200 +@@ -318,8 +318,8 @@ + if (element.NumElements() == 0) { + return Status::OK(); + } +- auto element_t = element.tensor(); +- auto parent_t = parent->tensor(); ++ auto element_t = element.template tensor(); ++ auto parent_t = parent->template tensor(); + Eigen::DSizes slice_indices; + slice_indices[0] = index; + Eigen::DSizes slice_size; +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/pad_op.cc tensorflow-1.8.0/tensorflow/core/kernels/pad_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/pad_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/pad_op.cc 2018-04-30 17:58:27.420248349 +0200 +@@ -216,7 +216,7 @@ + // Invoke the dims-specific implementation. + switch (fixed_dims) { + case 0: +- Operate<0>(context, input.tensor(), paddings, pad_value, output); ++ Operate<0>(context, input.template tensor(), paddings, pad_value, output); + break; + case 1: + // TODO(irving): Once Pad doesn't need a scalar special case, +@@ -224,19 +224,19 @@ + Operate<1>(context, input.flat(), paddings, pad_value, output); + break; + case 2: +- Operate<2>(context, input.tensor(), paddings, pad_value, output); ++ Operate<2>(context, input.template tensor(), paddings, pad_value, output); + break; + case 3: +- Operate<3>(context, input.tensor(), paddings, pad_value, output); ++ Operate<3>(context, input.template tensor(), paddings, pad_value, output); + break; + case 4: +- Operate<4>(context, input.tensor(), paddings, pad_value, output); ++ Operate<4>(context, input.template tensor(), paddings, pad_value, output); + break; + case 5: +- Operate<5>(context, input.tensor(), paddings, pad_value, output); ++ Operate<5>(context, input.template tensor(), paddings, pad_value, output); + break; + case 6: +- Operate<6>(context, input.tensor(), paddings, pad_value, output); ++ Operate<6>(context, input.template tensor(), paddings, pad_value, output); + break; + default: + OP_REQUIRES(context, false, +@@ -257,7 +257,7 @@ + paddings_array[i] = {paddings(i, 0), paddings(i, 1)}; + } + functor::Pad functor; +- functor(context->eigen_device(), output->tensor(), input, ++ functor(context->eigen_device(), output->template tensor(), input, + paddings_array, pad_value); + } + }; +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/pooling_ops_3d.cc tensorflow-1.8.0/tensorflow/core/kernels/pooling_ops_3d.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/pooling_ops_3d.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/pooling_ops_3d.cc 2018-04-30 17:58:27.704246623 +0200 +@@ -105,8 +105,8 @@ + const std::array& padding, + TensorFormat data_format, Padding padding_type, + Tensor* output) { +- output->tensor().device(context->eigen_device()) = +- Eigen::CuboidAvgPooling(tensor_in.tensor(), window[0], window[1], ++ output->template tensor().device(context->eigen_device()) = ++ Eigen::CuboidAvgPooling(tensor_in.template tensor(), window[0], window[1], + window[2], stride[0], stride[1], stride[2], + BrainPadding2EigenPadding(padding_type)); + } +@@ -120,8 +120,8 @@ + const std::array& padding, + TensorFormat data_format, Padding padding_type, + Tensor* output) { +- output->tensor().device(context->eigen_device()) = +- Eigen::CuboidMaxPooling(tensor_in.tensor(), window[0], window[1], ++ output->template tensor().device(context->eigen_device()) = ++ Eigen::CuboidMaxPooling(tensor_in.template tensor(), window[0], window[1], + window[2], stride[0], stride[1], stride[2], + BrainPadding2EigenPadding(padding_type)); + } +@@ -268,17 +268,17 @@ + // Slice from tensor_in. + Eigen::Tensor tensor_in_slice(dst_sizes); + tensor_in_slice.device(context->eigen_cpu_device()) = +- tensor_in.tensor().slice(dst_indices, dst_sizes); ++ tensor_in.template tensor().slice(dst_indices, dst_sizes); + + // Slice from tensor_out. + Eigen::Tensor tensor_out_slice(src_sizes); + tensor_out_slice.device(context->eigen_cpu_device()) = +- tensor_out.tensor().slice(src_indices, src_sizes); ++ tensor_out.template tensor().slice(src_indices, src_sizes); + + // Backprop slice. + Eigen::Tensor out_backprop_slice(src_sizes); + out_backprop_slice.device(context->eigen_cpu_device()) = +- out_backprop.tensor().slice(src_indices, src_sizes); ++ out_backprop.template tensor().slice(src_indices, src_sizes); + + // The true backprop slice: if an element is the max, choose + // the backprop slice; otherwise set to 0. +@@ -290,7 +290,7 @@ + tensor_in_slice.constant(1e-5)) + .select(out_backprop_slice.broadcast(bcast), mat0); + +- output->tensor() ++ output->template tensor() + .slice(dst_indices, dst_sizes) + .device(context->eigen_cpu_device()) += select_slice; + } +@@ -439,12 +439,12 @@ + #endif + Eigen::Tensor slices(src_sizes); + slices.device(context->eigen_cpu_device()) = +- out_backprop.tensor().slice(src_indices, src_sizes); ++ out_backprop.template tensor().slice(src_indices, src_sizes); + // Divide by the size of the actual patch (psize * rsize * csize). + float divide_size = rsize * csize * psize * 1.0f; + slices *= slices.constant(1.0f / divide_size); + +- output->tensor() ++ output->template tensor() + .slice(dst_indices, dst_sizes) + .device(context->eigen_cpu_device()) += slices.broadcast(bcast); + } +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/pooling_ops_common.cc tensorflow-1.8.0/tensorflow/core/kernels/pooling_ops_common.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/pooling_ops_common.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/pooling_ops_common.cc 2018-04-30 17:58:27.824245894 +0200 +@@ -167,8 +167,8 @@ + data_format), + &transformed_input)); + functor::NHWCToNCHW()(context->eigen_device(), +- tensor_in.tensor(), +- transformed_input.tensor()); ++ tensor_in.template tensor(), ++ transformed_input.template tensor()); + } else { + transformed_input = tensor_in; + } +@@ -230,7 +230,7 @@ + functor::NCHWToNHWC()( + context->eigen_device(), + toConstTensor(transformed_output).template tensor(), +- tensor_out->tensor()); ++ tensor_out->template tensor()); + } + } + +@@ -310,20 +310,20 @@ + // cudnn still requires them to run, although they do not affect the + // results. + functor::NHWCToNCHW()(context->eigen_device(), +- tensor_in->tensor(), +- transformed_input.tensor()); ++ tensor_in->template tensor(), ++ transformed_input.template tensor()); + } + if (tensor_out) { + // For AvgPoolGrad, the original output tensor is not necessary. However, + // cudnn still requires them to run, although they do not affect the + // results. + functor::NHWCToNCHW()(context->eigen_device(), +- tensor_out->tensor(), +- transformed_output.tensor()); ++ tensor_out->template tensor(), ++ transformed_output.template tensor()); + } + functor::NHWCToNCHW()( +- context->eigen_device(), out_backprop.tensor(), +- transformed_output_backprop.tensor()); ++ context->eigen_device(), out_backprop.template tensor(), ++ transformed_output_backprop.template tensor()); + } + + /// Get ready to call cudnn +@@ -382,7 +382,7 @@ + functor::NCHWToNHWC()( + context->eigen_device(), + toConstTensor(transformed_input_backprop).template tensor(), +- input_backprop->tensor()); ++ input_backprop->template tensor()); + } + } + +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/pooling_ops_common.h tensorflow-1.8.0/tensorflow/core/kernels/pooling_ops_common.h +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/pooling_ops_common.h 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/pooling_ops_common.h 2018-04-30 17:58:27.848245749 +0200 +@@ -164,8 +164,8 @@ + if (std::is_same::value) { + Eigen::PaddingType pt = BrainPadding2EigenPadding(padding); + functor::SpatialMaxPooling()( +- context->eigen_device(), output->tensor(), +- tensor_in.tensor(), params.window_rows, params.window_cols, ++ context->eigen_device(), output->template tensor(), ++ tensor_in.template tensor(), params.window_rows, params.window_cols, + params.row_stride, params.col_stride, pt); + } else { + typedef Eigen::Map> +@@ -408,8 +408,8 @@ + context, params, tensor_in, output); + } else { + functor::SpatialMaxPooling()( +- context->eigen_device(), output->tensor(), +- tensor_in.tensor(), params.window_rows, params.window_cols, ++ context->eigen_device(), output->template tensor(), ++ tensor_in.template tensor(), params.window_rows, params.window_cols, + params.row_stride, params.col_stride, pt); + } + } else +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/quantized_batch_norm_op_test.cc tensorflow-1.8.0/tensorflow/core/kernels/quantized_batch_norm_op_test.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/quantized_batch_norm_op_test.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/quantized_batch_norm_op_test.cc 2018-04-30 17:58:28.532241593 +0200 +@@ -226,10 +226,10 @@ + const Tensor& const_beta_float = beta_float; + const Tensor& const_gamma_float = gamma_float; + functor::BatchNorm()( +- eigen_cpu_device, const_input_float.tensor(), ++ eigen_cpu_device, const_input_float.template tensor(), + const_mean_float.vec(), const_variance_float.vec(), + const_beta_float.vec(), const_gamma_float.vec(), 0.001, +- false, expected_float.tensor()); ++ false, expected_float.template tensor()); + + const Tensor& output_quantized = *GetOutput(0); + const float output_min = GetOutput(1)->flat()(0); +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/quantized_concat_op.cc tensorflow-1.8.0/tensorflow/core/kernels/quantized_concat_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/quantized_concat_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/quantized_concat_op.cc 2018-04-30 17:58:28.604241156 +0200 +@@ -151,7 +151,7 @@ + if (in.NumElements() > 0) { + int64 inputs_flat_dim1 = in.NumElements() / inputs_flat_dim0; + inputs_flat->emplace_back(new typename TTypes::ConstMatrix( +- in.shaped({inputs_flat_dim0, inputs_flat_dim1}))); ++ in.template shaped({inputs_flat_dim0, inputs_flat_dim1}))); + } + *output_concat_dim += in.dims() > 0 ? in.dim_size(concat_dim) : 1; + } +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/quantized_instance_norm.cc tensorflow-1.8.0/tensorflow/core/kernels/quantized_instance_norm.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/quantized_instance_norm.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/quantized_instance_norm.cc 2018-04-30 17:58:28.700240572 +0200 +@@ -283,7 +283,7 @@ + "input_min must be less than input_max : ", input_min, + " >= ", input_max)); + +- auto input_tensor = input.tensor(); ++ auto input_tensor = input.template tensor(); + auto N = input_tensor.dimension(0); + auto H = input_tensor.dimension(1); + auto W = input_tensor.dimension(2); +@@ -385,7 +385,7 @@ + auto instance_normed_quantized = + QUANTIZE_WITH_EIGEN(instance_normed, output_f2q, quint8); + +- output->tensor().device( ++ output->template tensor().device( + context->template eigen_device()) = + instance_normed_quantized; + output_min->flat()(0) = normed_min(); +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/quantized_resize_bilinear_op.cc tensorflow-1.8.0/tensorflow/core/kernels/quantized_resize_bilinear_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/quantized_resize_bilinear_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/quantized_resize_bilinear_op.cc 2018-04-30 17:58:28.940239114 +0200 +@@ -697,8 +697,8 @@ + // Return if the output is empty. + if (st.output->NumElements() == 0) return; + +- typename TTypes::ConstTensor image_data(input.tensor()); +- typename TTypes::Tensor output_data(st.output->tensor()); ++ typename TTypes::ConstTensor image_data(input.template tensor()); ++ typename TTypes::Tensor output_data(st.output->template tensor()); + + ResizeBilinear(image_data, st.height_scale, st.width_scale, in_min, + in_max, &output_data); +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/random_crop_op.cc tensorflow-1.8.0/tensorflow/core/kernels/random_crop_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/random_crop_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/random_crop_op.cc 2018-04-30 17:58:29.080238264 +0200 +@@ -92,8 +92,8 @@ + + // TODO(shlens): Do this more efficiently with memcpy once padding is + // available for smaller images. +- typename TTypes::ConstTensor input_data(input.tensor()); +- typename TTypes::Tensor output_data(output->tensor()); ++ typename TTypes::ConstTensor input_data(input.template tensor()); ++ typename TTypes::Tensor output_data(output->template tensor()); + + for (int y = 0; y < target_height; ++y) { + for (int x = 0; x < target_width; ++x) { +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/reduction_ops_common.h tensorflow-1.8.0/tensorflow/core/kernels/reduction_ops_common.h +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/reduction_ops_common.h 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/reduction_ops_common.h 2018-04-30 17:58:29.628234934 +0200 +@@ -109,7 +109,7 @@ + // The input is reshaped. + template + typename TTypes::ConstTensor in(const Tensor& data) { +- return data.shaped(data_reshape_); ++ return data.template shaped(data_reshape_); + } + + // Shape of shuffled input +@@ -228,7 +228,7 @@ + const int64 reduced = shuffled.NumElements() / unreduced; + const Tensor& const_shuffled = shuffled; + Functor::Reduce(ctx, tmp_out.flat(), +- const_shuffled.shaped({unreduced, reduced}), ++ const_shuffled.template shaped({unreduced, reduced}), + constants.kOne, reducer); + } + +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/resize_area_op.cc tensorflow-1.8.0/tensorflow/core/kernels/resize_area_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/resize_area_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/resize_area_op.cc 2018-04-30 17:58:30.520229515 +0200 +@@ -149,7 +149,7 @@ + + if (!context->status().ok()) return; + +- typename TTypes::ConstTensor input_data(input.tensor()); ++ typename TTypes::ConstTensor input_data(input.template tensor()); + + // Precompute values used when iterating over x coordinates within a row. + // Note that it may be useful to cache x_interps for a given +@@ -190,7 +190,7 @@ + void ComputeLoop(const ImageResizerState& st, + const std::vector& x_interps, + typename TTypes::ConstTensor input_data) { +- TTypes::Tensor output_data = st.output->tensor(); ++ TTypes::Tensor output_data = st.output->template tensor(); + + // When using this algorithm for downsizing, the target pixel value is the + // weighted average of all the source pixels. The weight is determined by +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/resize_area_op_test.cc tensorflow-1.8.0/tensorflow/core/kernels/resize_area_op_test.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/resize_area_op_test.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/resize_area_op_test.cc 2018-04-30 17:58:30.540229394 +0200 +@@ -153,7 +153,7 @@ + new Tensor(device_->GetAllocator(AllocatorAttributes()), + DataTypeToEnum::v(), + TensorShape({1, target_height, target_width, channels}))); +- ResizeAreaBaseline(input->tensor(), expected->tensor()); ++ ResizeAreaBaseline(input->template tensor(), expected->template tensor()); + test::ExpectTensorNear(*expected, *GetOutput(0), 0.00001); + } + +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/resize_bicubic_op.cc tensorflow-1.8.0/tensorflow/core/kernels/resize_bicubic_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/resize_bicubic_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/resize_bicubic_op.cc 2018-04-30 17:58:30.568229224 +0200 +@@ -480,8 +480,8 @@ + + if (!context->status().ok()) return; + +- typename TTypes::ConstTensor input_data(input.tensor()); +- TTypes::Tensor output_data = st.output->tensor(); ++ typename TTypes::ConstTensor input_data(input.template tensor()); ++ TTypes::Tensor output_data = st.output->template tensor(); + + interpolate_with_caching(input_data, st, output_data); + } +@@ -509,8 +509,8 @@ + + if (!context->status().ok()) return; + +- TTypes::ConstTensor input_grad = input.tensor(); +- typename TTypes::Tensor output_grad(st.output->tensor()); ++ TTypes::ConstTensor input_grad = input.template tensor(); ++ typename TTypes::Tensor output_grad(st.output->template tensor()); + + ResizeBicubicGrad(input_grad, st, output_grad); + } +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/resize_bicubic_op_test.cc tensorflow-1.8.0/tensorflow/core/kernels/resize_bicubic_op_test.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/resize_bicubic_op_test.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/resize_bicubic_op_test.cc 2018-04-30 17:58:30.592229078 +0200 +@@ -173,8 +173,8 @@ + DataTypeToEnum::v(), + TensorShape({batch_size, target_height, target_width, channels}))); + +- ResizeBicubicBaseline(input->tensor(), +- expected->tensor()); ++ ResizeBicubicBaseline(input->template tensor(), ++ expected->template tensor()); + // Note: the baseline implementation reduces first in the x direction, and + // then in the y direction. The optimized version reduces first in the y + // direction, and then the X direction. As a result, there may be +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/resize_bilinear_op.cc tensorflow-1.8.0/tensorflow/core/kernels/resize_bilinear_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/resize_bilinear_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/resize_bilinear_op.cc 2018-04-30 17:58:30.616228932 +0200 +@@ -51,8 +51,8 @@ + // Return if the output is empty. + if (st.output->NumElements() == 0) return; + +- typename TTypes::ConstTensor image_data(input.tensor()); +- TTypes::Tensor output_data = st.output->tensor(); ++ typename TTypes::ConstTensor image_data(input.template tensor()); ++ TTypes::Tensor output_data = st.output->template tensor(); + + functor::ResizeBilinear()(context->eigen_device(), + image_data, st.height_scale, +@@ -257,8 +257,8 @@ + + if (!context->status().ok()) return; + +- TTypes::ConstTensor input_grad = input.tensor(); +- typename TTypes::Tensor output_grad(st.output->tensor()); ++ TTypes::ConstTensor input_grad = input.template tensor(); ++ typename TTypes::Tensor output_grad(st.output->template tensor()); + + functor::ResizeBilinearGrad()(context->eigen_device(), + input_grad, st.height_scale, +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/resize_bilinear_op_test.cc tensorflow-1.8.0/tensorflow/core/kernels/resize_bilinear_op_test.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/resize_bilinear_op_test.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/resize_bilinear_op_test.cc 2018-04-30 17:58:30.688228495 +0200 +@@ -120,8 +120,8 @@ + device_->GetAllocator(AllocatorAttributes()), + DataTypeToEnum::v(), + TensorShape({batch_size, output_width, output_height, channels}))); +- ResizeBilinearBaseline(input->tensor(), +- expected->tensor()); ++ ResizeBilinearBaseline(input->template tensor(), ++ expected->template tensor()); + test::ExpectTensorEqual(*expected, *GetOutput(0)); + } + +@@ -191,8 +191,8 @@ + std::unique_ptr expected( + new Tensor(device_->GetAllocator(AllocatorAttributes()), + DataTypeToEnum::v(), TensorShape({1, 1, 1, 1}))); +- ResizeBilinearBaseline(input->tensor(), +- expected->tensor()); ++ ResizeBilinearBaseline(input->template tensor(), ++ expected->template tensor()); + EXPECT_EQ(input->flat()(0), output->flat()(0)); + test::ExpectTensorEqual(*expected, *output); + } +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/resize_nearest_neighbor_op.cc tensorflow-1.8.0/tensorflow/core/kernels/resize_nearest_neighbor_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/resize_nearest_neighbor_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/resize_nearest_neighbor_op.cc 2018-04-30 17:58:30.712228349 +0200 +@@ -56,8 +56,8 @@ + // Return if the output is empty. + if (st.output->NumElements() == 0) return; + +- typename TTypes::ConstTensor input_data(input.tensor()); +- typename TTypes::Tensor output_data(st.output->tensor()); ++ typename TTypes::ConstTensor input_data(input.template tensor()); ++ typename TTypes::Tensor output_data(st.output->template tensor()); + + bool status; + if (align_corners_) { +@@ -162,8 +162,8 @@ + // Return if the output is empty. + if (output->NumElements() == 0) return; + +- typename TTypes::ConstTensor input_data(input.tensor()); +- typename TTypes::Tensor output_data(output->tensor()); ++ typename TTypes::ConstTensor input_data(input.template tensor()); ++ typename TTypes::Tensor output_data(output->template tensor()); + + const float height_scale = + CalculateResizeScale(out_height, in_height, align_corners_); +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/resource_variable_ops.cc tensorflow-1.8.0/tensorflow/core/kernels/resource_variable_ops.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/resource_variable_ops.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/resource_variable_ops.cc 2018-04-30 17:58:30.828227644 +0200 +@@ -444,7 +444,7 @@ + Tensor* output = nullptr; + OP_REQUIRES_OK(context, + context->allocate_output(0, TensorShape({}), &output)); +- auto output_tensor = output->tensor(); ++ auto output_tensor = output->template tensor(); + Var* variable = nullptr; + Status s = LookupResource(context, HandleFromInput(context, 0), &variable); + if (!s.ok()) { +@@ -519,7 +519,7 @@ + for (int i = 1; i < params.dims(); i++) { + inner_size *= params.dim_size(i); + } +- auto params_flat = params.shaped({1, gather_dim_size, inner_size}); ++ auto params_flat = params.template shaped({1, gather_dim_size, inner_size}); + auto indices_flat = indices.flat(); + auto out_flat = out->shaped({1, N, out->NumElements() / N}); + +@@ -635,7 +635,7 @@ + "shape of indices (", indices.shape().DebugString(), + ") is not compatible with the shape of updates (", + updates.shape().DebugString(), ")")); +- auto updates_flat = updates.shaped({N, num_updates / N}); ++ auto updates_flat = updates.template shaped({N, num_updates / N}); + + functor::ScatterFunctor functor; + const Index bad_i = functor(c, c->template eigen_device(), +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/reverse_op.cc tensorflow-1.8.0/tensorflow/core/kernels/reverse_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/reverse_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/reverse_op.cc 2018-04-30 17:58:30.928227037 +0200 +@@ -147,8 +147,8 @@ + axes_di[i] = dims(i); + } + functor::Reverse()(context->eigen_device(), +- input.tensor(), axes_di, +- result->tensor()); ++ input.template tensor(), axes_di, ++ result->template tensor()); + } + + template +@@ -224,8 +224,8 @@ + axes_di[i] = axes[i]; + } + functor::Reverse()(context->eigen_device(), +- input.tensor(), axes_di, +- result->tensor()); ++ input.template tensor(), axes_di, ++ result->template tensor()); + } + + template +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/reverse_sequence_op.cc tensorflow-1.8.0/tensorflow/core/kernels/reverse_sequence_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/reverse_sequence_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/reverse_sequence_op.cc 2018-04-30 17:58:31.020226478 +0200 +@@ -137,8 +137,8 @@ + #define HANDLE_DIM(NDIM) \ + case NDIM: \ + functor::ReverseSequence::Compute( \ +- context->eigen_device(), input.tensor(), batch_dim_, \ +- seq_dim_, seq_lens_t, output->tensor()); \ ++ context->eigen_device(), input.template tensor(), batch_dim_, \ ++ seq_dim_, seq_lens_t, output->template tensor()); \ + break; + + switch (input_dims) { +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/sample_distorted_bounding_box_op.cc tensorflow-1.8.0/tensorflow/core/kernels/sample_distorted_bounding_box_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/sample_distorted_bounding_box_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/sample_distorted_bounding_box_op.cc 2018-04-30 17:58:31.164225603 +0200 +@@ -387,9 +387,9 @@ + OP_REQUIRES_OK( + context, context->allocate_output(2, TensorShape({1, 1, 4}), &bboxes)); + +- typename TTypes::Tensor begin_data(begin->tensor()); +- typename TTypes::Tensor size_data(size->tensor()); +- TTypes::Tensor bboxes_data = bboxes->tensor(); ++ typename TTypes::Tensor begin_data(begin->template tensor()); ++ typename TTypes::Tensor size_data(size->template tensor()); ++ TTypes::Tensor bboxes_data = bboxes->template tensor(); + + begin_data(0) = T(offset_height); + size_data(0) = T(target_height); +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/scan_ops.cc tensorflow-1.8.0/tensorflow/core/kernels/scan_ops.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/scan_ops.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/scan_ops.cc 2018-04-30 17:58:31.332224583 +0200 +@@ -79,7 +79,7 @@ + reduced_shape[2] *= input.dim_size(i); + } + +- functor::Scan()(d, input.shaped(reduced_shape), ++ functor::Scan()(d, input.template shaped(reduced_shape), + output->shaped(reduced_shape), + reducer, reverse_, exclusive_); + } +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/scatter_nd_op.cc tensorflow-1.8.0/tensorflow/core/kernels/scatter_nd_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/scatter_nd_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/scatter_nd_op.cc 2018-04-30 17:58:31.496223586 +0200 +@@ -445,7 +445,7 @@ + + IndexFlattener index_flattener; + auto indices_flat = index_flattener(c, indices); +- auto updates_flat = updates.shaped({num_updates, slice_size}); ++ auto updates_flat = updates.template shaped({num_updates, slice_size}); + + if (allocate) { + TF_RETURN_IF_ERROR(c->allocate_temp(DataTypeToEnum::value, shape, out)); +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/scatter_op.cc tensorflow-1.8.0/tensorflow/core/kernels/scatter_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/scatter_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/scatter_op.cc 2018-04-30 17:58:31.796221764 +0200 +@@ -137,7 +137,7 @@ + params.dim_size(0), ")")); + } else { + auto updates_flat = +- updates.shaped({N, updates.NumElements() / N}); ++ updates.template shaped({N, updates.NumElements() / N}); + + functor::ScatterFunctor functor; + const Index bad_i = functor(c, c->template eigen_device(), +@@ -225,7 +225,7 @@ + params.dim_size(0), ")")); + } else { + auto updates_flat = +- updates.shaped({N, updates.NumElements() / N}); ++ updates.template shaped({N, updates.NumElements() / N}); + + functor::ScatterFunctorSYCL functor; + const Index bad_i = functor(c, c->template eigen_device(), +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/sdca_internal.cc tensorflow-1.8.0/tensorflow/core/kernels/sdca_internal.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/sdca_internal.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/sdca_internal.cc 2018-04-30 17:58:31.916221035 +0200 +@@ -114,7 +114,7 @@ + deltas.setZero(); + sparse_weights_.emplace_back(FeatureWeightsSparseStorage{ + sparse_indices_inputs[i].flat(), +- sparse_weights_inputs[i].shaped( ++ sparse_weights_inputs[i].template shaped( + {1, sparse_weights_inputs[i].NumElements()}), + deltas}); + } +@@ -132,7 +132,7 @@ + auto deltas = delta_t->shaped({1, delta_t->NumElements()}); + deltas.setZero(); + feature_weights->emplace_back(FeatureWeightsDenseStorage{ +- weight_inputs[i].shaped( ++ weight_inputs[i].template shaped( + {1, weight_inputs[i].NumElements()}), + deltas}); + } +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/slice_op.cc tensorflow-1.8.0/tensorflow/core/kernels/slice_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/slice_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/slice_op.cc 2018-04-30 17:58:32.532217293 +0200 +@@ -175,8 +175,8 @@ + if (output_shape.num_elements() > 0) { + if (std::is_same::value && input_dims == 2 && + DataTypeCanUseMemcpy(DataTypeToEnum::v())) { +- auto input = context->input(0).tensor(); +- auto output = result->tensor(); ++ auto input = context->input(0).template tensor(); ++ auto output = result->template tensor(); + // TODO(agarwal): Consider multi-threading this loop for cases where + // size[0] is very large. + for (int i = 0; i < size[0]; ++i) { +@@ -223,8 +223,8 @@ + } + + functor::Slice()( +- context->eigen_device(), result->tensor(), +- context->input(0).tensor(), indices, sizes); ++ context->eigen_device(), result->template tensor(), ++ context->input(0).template tensor(), indices, sizes); + } + }; + +@@ -250,8 +250,8 @@ + if (output_shape.num_elements() > 0) { + if (std::is_same::value && input_dims == 2 && + DataTypeCanUseMemcpy(DataTypeToEnum::v())) { +- auto input = context->input(0).tensor(); +- auto output = result->tensor(); ++ auto input = context->input(0).template tensor(); ++ auto output = result->template tensor(); + // TODO(agarwal): Consider multi-threading this loop for cases where + // size[0] is very large. + for (int i = 0; i < size[0]; ++i) { +@@ -407,8 +407,8 @@ + } + + functor::Slice()( +- context->eigen_device(), result->tensor(), +- context->input(0).tensor(), indices, sizes); ++ context->eigen_device(), result->template tensor(), ++ context->input(0).template tensor(), indices, sizes); + } + }; + #endif +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/spacetobatch_op.cc tensorflow-1.8.0/tensorflow/core/kernels/spacetobatch_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/spacetobatch_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/spacetobatch_op.cc 2018-04-30 17:58:33.196213259 +0200 +@@ -187,7 +187,7 @@ + context, \ + (functor::SpaceToBatchFunctor()( \ + context->eigen_device(), \ +- orig_input_tensor.shaped( \ ++ orig_input_tensor.template shaped( \ + internal_input_shape.dim_sizes()), \ + internal_block_shape, internal_paddings, \ + output_tensor->shaped( \ +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/spacetodepth_op.cc tensorflow-1.8.0/tensorflow/core/kernels/spacetodepth_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/spacetodepth_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/spacetodepth_op.cc 2018-04-30 17:58:33.220213113 +0200 +@@ -111,8 +111,8 @@ + output_width, output_depth), + &outputs_tensor)); + +- auto Tinput = input.tensor(); +- auto Toutput = outputs_tensor->tensor(); ++ auto Tinput = input.template tensor(); ++ auto Toutput = outputs_tensor->template tensor(); + + if (std::is_same::value) { + if (is_int8x4) { +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/sparse_tensor_dense_add_op.cc tensorflow-1.8.0/tensorflow/core/kernels/sparse_tensor_dense_add_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/sparse_tensor_dense_add_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/sparse_tensor_dense_add_op.cc 2018-04-30 17:58:33.792209639 +0200 +@@ -90,8 +90,8 @@ + switch (ndims) { + #define NDIMS_CASE(N) \ + case N: { \ +- auto out_tensor = out_t->tensor(); \ +- out_tensor.device(ctx->eigen_device()) = b->tensor(); \ ++ auto out_tensor = out_t->template tensor(); \ ++ out_tensor.device(ctx->eigen_device()) = b->template tensor(); \ + const Index result = \ + functor::ScatterNdFunctor()( \ +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/sparse_to_dense_op.cc tensorflow-1.8.0/tensorflow/core/kernels/sparse_to_dense_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/sparse_to_dense_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/sparse_to_dense_op.cc 2018-04-30 17:58:33.956208642 +0200 +@@ -99,7 +99,7 @@ + CHECK(indices_shaped.CopyFrom(indices, ix_shape)); + } else { + indices_shaped.matrix() = +- indices.shaped(ix_shape.dim_sizes()).template cast(); ++ indices.template shaped(ix_shape.dim_sizes()).template cast(); + } + + // If we received a scalar, we'll need to create a new +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/sparse_to_dense_op_test.cc tensorflow-1.8.0/tensorflow/core/kernels/sparse_to_dense_op_test.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/sparse_to_dense_op_test.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/sparse_to_dense_op_test.cc 2018-04-30 17:58:33.980208497 +0200 +@@ -122,9 +122,9 @@ + + Tensor expected(allocator(), DT_FLOAT, {3, 4}); + expected.flat().setConstant(-2); +- expected.tensor()(0, 1) = 2; +- expected.tensor()(0, 2) = 2; +- expected.tensor()(2, 3) = 2; ++ expected.template tensor()(0, 1) = 2; ++ expected.template tensor()(0, 2) = 2; ++ expected.template tensor()(2, 3) = 2; + test::ExpectTensorEqual(expected, *GetOutput(0)); + } + +@@ -144,9 +144,9 @@ + + Tensor expected(allocator(), DT_FLOAT, {3, 4}); + expected.flat().setConstant(-2); +- expected.tensor()(0, 1) = 3; +- expected.tensor()(0, 2) = 4; +- expected.tensor()(2, 3) = 5; ++ expected.template tensor()(0, 1) = 3; ++ expected.template tensor()(0, 2) = 4; ++ expected.template tensor()(2, 3) = 5; + test::ExpectTensorEqual(expected, *GetOutput(0)); + } + +@@ -166,9 +166,9 @@ + + Tensor expected(allocator(), DT_FLOAT, {3, 4, 2}); + expected.flat().setConstant(-2); +- expected.tensor()(0, 1, 1) = 2; +- expected.tensor()(0, 2, 0) = 2; +- expected.tensor()(2, 3, 1) = 2; ++ expected.template tensor()(0, 1, 1) = 2; ++ expected.template tensor()(0, 2, 0) = 2; ++ expected.template tensor()(2, 3, 1) = 2; + test::ExpectTensorEqual(expected, *GetOutput(0)); + } + +@@ -188,9 +188,9 @@ + + Tensor expected(allocator(), DT_FLOAT, {3, 4, 2}); + expected.flat().setConstant(-2); +- expected.tensor()(0, 1, 1) = 3; +- expected.tensor()(0, 2, 0) = 4; +- expected.tensor()(2, 3, 1) = 5; ++ expected.template tensor()(0, 1, 1) = 3; ++ expected.template tensor()(0, 2, 0) = 4; ++ expected.template tensor()(2, 3, 1) = 5; + test::ExpectTensorEqual(expected, *GetOutput(0)); + } + +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/split_op.cc tensorflow-1.8.0/tensorflow/core/kernels/split_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/split_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/split_op.cc 2018-04-30 17:58:34.488205411 +0200 +@@ -230,7 +230,7 @@ + + if (prefix_dim_size == 1) { + auto input_reshaped = +- input.shaped({split_dim_size, suffix_dim_size}); ++ input.template shaped({split_dim_size, suffix_dim_size}); + auto make_sizes = [&](Eigen::DenseIndex split_size) { + return Eigen::DSizes{split_size, suffix_dim_size}; + }; +@@ -242,7 +242,7 @@ + split_dim_size, suffix_dim_size, make_sizes, reshape_result, + num_split, split_dim_output_size); + } else { +- auto input_reshaped = input.shaped( ++ auto input_reshaped = input.template shaped( + {prefix_dim_size, split_dim_size, suffix_dim_size}); + auto make_sizes = [&](Eigen::DenseIndex split_size) { + return Eigen::DSizes{prefix_dim_size, split_size, +@@ -361,7 +361,7 @@ + std::tie(prefix_dim_size, split_dim_size, suffix_dim_size) = + Base::template SetDims(input_shape, split_dim); + auto input_reshaped = +- input.shaped({prefix_dim_size, split_dim_size, suffix_dim_size}); ++ input.template shaped({prefix_dim_size, split_dim_size, suffix_dim_size}); + + const int64 split_dim_output_size = split_dim_size / num_split; + TensorShape output_shape(input_shape); +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/split_v_op.cc tensorflow-1.8.0/tensorflow/core/kernels/split_v_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/split_v_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/split_v_op.cc 2018-04-30 17:58:34.536205119 +0200 +@@ -297,7 +297,7 @@ + + if (prefix_dim_size == 1) { + auto input_reshaped = +- input.shaped({split_dim_size, suffix_dim_size}); ++ input.template shaped({split_dim_size, suffix_dim_size}); + auto make_sizes = [&](Eigen::DenseIndex split_size) { + return Eigen::DSizes{split_size, suffix_dim_size}; + }; +@@ -309,7 +309,7 @@ + prefix_dim_size, split_dim_size, suffix_dim_size, split_sizes_vec, + make_sizes, reshape_result); + } else { +- auto input_reshaped = input.shaped( ++ auto input_reshaped = input.template shaped( + {prefix_dim_size, split_dim_size, suffix_dim_size}); + auto make_sizes = [&](Eigen::DenseIndex split_size) { + return Eigen::DSizes{prefix_dim_size, split_size, +@@ -415,7 +415,7 @@ + + std::tie(prefix_dim_size, split_dim_size, suffix_dim_size) = + Base::template SetDims(input_shape, split_dim); +- auto input_reshaped = input.shaped( ++ auto input_reshaped = input.template shaped( + {prefix_dim_size, split_dim_size * suffix_dim_size}); + + Eigen::DSizes indices{0, 0}; +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/strided_slice_op.cc tensorflow-1.8.0/tensorflow/core/kernels/strided_slice_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/strided_slice_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/strided_slice_op.cc 2018-04-30 17:58:34.680204244 +0200 +@@ -47,8 +47,8 @@ + bool Copy(const Tensor& input, const gtl::InlinedVector& begin, + const gtl::InlinedVector& end, Tensor* result) { + if (DataTypeCanUseMemcpy(DataTypeToEnum::v())) { +- auto in = input.tensor(); +- auto output = result->tensor(); ++ auto in = input.template tensor(); ++ auto output = result->template tensor(); + // TODO(agarwal): Consider multi-threading if size[0] is large + for (int row_in = begin[0], row_out = 0; row_in < end[0]; + ++row_in, ++row_out) { +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/substr_op.cc tensorflow-1.8.0/tensorflow/core/kernels/substr_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/substr_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/substr_op.cc 2018-04-30 17:58:35.116201596 +0200 +@@ -106,17 +106,17 @@ + switch (ndims) { + case 1: { + // Reshape tensors according to BCast results +- auto input = input_tensor.shaped(bcast.x_reshape()); ++ auto input = input_tensor.template shaped(bcast.x_reshape()); + auto output = output_tensor->shaped(bcast.result_shape()); +- auto pos_shaped = pos_tensor.shaped(bcast.y_reshape()); +- auto len_shaped = len_tensor.shaped(bcast.y_reshape()); ++ auto pos_shaped = pos_tensor.template shaped(bcast.y_reshape()); ++ auto len_shaped = len_tensor.template shaped(bcast.y_reshape()); + + // Allocate temporary buffer for broadcasted input tensor + Tensor input_buffer; + OP_REQUIRES_OK(context, context->allocate_temp( + DT_STRING, output_shape, &input_buffer)); + TTypes::Tensor input_bcast = +- input_buffer.shaped(bcast.result_shape()); ++ input_buffer.template shaped(bcast.result_shape()); + input_bcast = + input.broadcast(BCast::ToIndexArray<1>(bcast.x_bcast())); + +@@ -126,7 +126,7 @@ + context->allocate_temp(DataTypeToEnum::v(), + output_shape, &pos_buffer)); + typename TTypes::Tensor pos_bcast( +- pos_buffer.shaped(bcast.result_shape())); ++ pos_buffer.template shaped(bcast.result_shape())); + pos_bcast = + pos_shaped.broadcast(BCast::ToIndexArray<1>(bcast.y_bcast())); + +@@ -136,7 +136,7 @@ + context->allocate_temp(DataTypeToEnum::v(), + output_shape, &len_buffer)); + typename TTypes::Tensor len_bcast( +- len_buffer.shaped(bcast.result_shape())); ++ len_buffer.template shaped(bcast.result_shape())); + len_bcast = + len_shaped.broadcast(BCast::ToIndexArray<1>(bcast.y_bcast())); + +@@ -155,17 +155,17 @@ + } + case 2: { + // Reshape tensors according to BCast results +- auto input = input_tensor.shaped(bcast.x_reshape()); ++ auto input = input_tensor.template shaped(bcast.x_reshape()); + auto output = output_tensor->shaped(bcast.result_shape()); +- auto pos_shaped = pos_tensor.shaped(bcast.y_reshape()); +- auto len_shaped = len_tensor.shaped(bcast.y_reshape()); ++ auto pos_shaped = pos_tensor.template shaped(bcast.y_reshape()); ++ auto len_shaped = len_tensor.template shaped(bcast.y_reshape()); + + // Allocate temporary buffer for broadcasted input tensor + Tensor input_buffer; + OP_REQUIRES_OK(context, context->allocate_temp( + DT_STRING, output_shape, &input_buffer)); + TTypes::Tensor input_bcast = +- input_buffer.shaped(bcast.result_shape()); ++ input_buffer.template shaped(bcast.result_shape()); + input_bcast = + input.broadcast(BCast::ToIndexArray<2>(bcast.x_bcast())); + +@@ -175,7 +175,7 @@ + context->allocate_temp(DataTypeToEnum::v(), + output_shape, &pos_buffer)); + typename TTypes::Tensor pos_bcast( +- pos_buffer.shaped(bcast.result_shape())); ++ pos_buffer.template shaped(bcast.result_shape())); + pos_bcast = + pos_shaped.broadcast(BCast::ToIndexArray<2>(bcast.y_bcast())); + +@@ -185,7 +185,7 @@ + context->allocate_temp(DataTypeToEnum::v(), + output_shape, &len_buffer)); + typename TTypes::Tensor len_bcast( +- len_buffer.shaped(bcast.result_shape())); ++ len_buffer.template shaped(bcast.result_shape())); + len_bcast = + len_shaped.broadcast(BCast::ToIndexArray<2>(bcast.y_bcast())); + +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/summary_audio_op.cc tensorflow-1.8.0/tensorflow/core/kernels/summary_audio_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/summary_audio_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/summary_audio_op.cc 2018-04-30 17:58:35.140201450 +0200 +@@ -76,7 +76,7 @@ + sa->set_content_type("audio/wav"); + + auto values = +- tensor.shaped({batch_size, length_frames, num_channels}); ++ tensor.template shaped({batch_size, length_frames, num_channels}); + auto channels_by_frames = typename TTypes::ConstMatrix( + &values(i, 0, 0), + Eigen::DSizes(length_frames, num_channels)); +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/summary_image_op.cc tensorflow-1.8.0/tensorflow/core/kernels/summary_image_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/summary_image_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/summary_image_op.cc 2018-04-30 17:58:35.184201183 +0200 +@@ -82,7 +82,7 @@ + if (tensor.dtype() == DT_UINT8) { + // For uint8 input, no normalization is necessary + auto ith_image = [&tensor, batch_size, hw, depth](int i) { +- auto values = tensor.shaped({batch_size, hw, depth}); ++ auto values = tensor.template shaped({batch_size, hw, depth}); + return typename TTypes::ConstMatrix( + &values(i, 0, 0), Eigen::DSizes(hw, depth)); + }; +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/tile_functor.h tensorflow-1.8.0/tensorflow/core/kernels/tile_functor.h +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/tile_functor.h 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/tile_functor.h 2018-04-30 17:58:35.636198437 +0200 +@@ -33,8 +33,8 @@ + template + void TileUsingEigen(const Device& d, Tensor* out, const Tensor& in, + const gtl::ArraySlice& broadcast_array) { +- auto x = in.tensor(); +- auto y = out->tensor(); ++ auto x = in.template tensor(); ++ auto y = out->template tensor(); + + Eigen::array b; + for (int i = 0; i < NDIM; ++i) b[i] = broadcast_array[i]; +@@ -49,8 +49,8 @@ + template + void TileUsingEigen(const Device& d, Tensor* out, const Tensor& in, + const gtl::ArraySlice&) { +- auto x = in.tensor(); +- auto y = out->tensor(); ++ auto x = in.template tensor(); ++ auto y = out->template tensor(); + // In the scalar case we simply copy the input. + y.device(d) = x; + } +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/tile_ops.cc tensorflow-1.8.0/tensorflow/core/kernels/tile_ops.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/tile_ops.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/tile_ops.cc 2018-04-30 17:58:35.704198024 +0200 +@@ -392,8 +392,8 @@ + bool first = true; + while (true) { + functor::TileGrad()( +- context->eigen_device(), result->tensor(), +- context->input(0).tensor(), indices, sizes, first); ++ context->eigen_device(), result->template tensor(), ++ context->input(0).template tensor(), indices, sizes, first); + first = false; + // Increment the begin indices. + int i = 0; +@@ -427,8 +427,8 @@ + } + + functor::ReduceAndReshape()( +- context->eigen_device(), result->tensor(), +- context->input(0).tensor(), reduce_dim, reshape_dim); ++ context->eigen_device(), result->template tensor(), ++ context->input(0).template tensor(), reduce_dim, reshape_dim); + } + + TF_DISALLOW_COPY_AND_ASSIGN(TileGradientOp); +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/transpose_op.cc tensorflow-1.8.0/tensorflow/core/kernels/transpose_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/transpose_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/transpose_op.cc 2018-04-30 17:58:36.440193554 +0200 +@@ -133,8 +133,8 @@ + // Specifically, the returned tensor output meets the following condition: + // 1) output.dims() == input.dims(); + // 2) output.dim_size(i) == input.dim_size(perm[i]); +-// 3) output.tensor(i_0, i_1, ..., i_N-1) == +-// input.tensor(j_0, j_1, ..., j_N-1), ++// 3) output.template tensor(i_0, i_1, ..., i_N-1) == ++// input.template tensor(j_0, j_1, ..., j_N-1), + // where i_s == j_{perm[s]} + // + // REQUIRES: perm is a vector of int32. +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/unique_op.cc tensorflow-1.8.0/tensorflow/core/kernels/unique_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/unique_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/unique_op.cc 2018-04-30 17:58:36.556192849 +0200 +@@ -129,7 +129,7 @@ + } + } else { + // General implementation when unique is run over multiple elements. +- auto Tin = input.shaped(new_sizes); ++ auto Tin = input.template shaped(new_sizes); + + auto hash_fn = [&Tin](const int64& key) { + size_t h = 0; +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/unpack_op.cc tensorflow-1.8.0/tensorflow/core/kernels/unpack_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/unpack_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/unpack_op.cc 2018-04-30 17:58:36.604192557 +0200 +@@ -104,7 +104,7 @@ + // Except for shape, unpack is a special case of split, so we reuse the + // same computational kernels. + auto input_reshaped = +- input.shaped({before_dim, axis_dim * after_dim}); ++ input.template shaped({before_dim, axis_dim * after_dim}); + + for (int i = 0; i < num; ++i) { + Tensor* output; +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/variable_ops.cc tensorflow-1.8.0/tensorflow/core/kernels/variable_ops.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/variable_ops.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/variable_ops.cc 2018-04-30 17:58:36.652192266 +0200 +@@ -171,7 +171,7 @@ + Tensor* output = nullptr; + OP_REQUIRES_OK(context, + context->allocate_output(0, TensorShape({}), &output)); +- auto output_tensor = output->tensor(); ++ auto output_tensor = output->template tensor(); + bool result = input_tensor.IsInitialized(); + output_tensor() = result; + } +diff -ru tensorflow-1.8.0.orig/tensorflow/core/kernels/where_op.cc tensorflow-1.8.0/tensorflow/core/kernels/where_op.cc +--- tensorflow-1.8.0.orig/tensorflow/core/kernels/where_op.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/kernels/where_op.cc 2018-04-30 17:58:36.768191561 +0200 +@@ -158,7 +158,7 @@ + #define HANDLE_DIM(NDIM) \ + case NDIM: { \ + Status s = functor::Where::Compute( \ +- context, context->eigen_device(), input.tensor(), \ ++ context, context->eigen_device(), input.template tensor(), \ + output->matrix(), &found_true); \ + OP_REQUIRES_OK(context, s); \ + } break; +@@ -322,7 +322,7 @@ + #define HANDLE_DIM(NDIM) \ + case NDIM: { \ + Status s = functor::Where::Compute( \ +- context, d, input.tensor(), output->matrix(), \ ++ context, d, input.template tensor(), output->matrix(), \ + &found_true); \ + OP_REQUIRES_OK_ASYNC(context, s, done); \ + } break; +diff -ru tensorflow-1.8.0.orig/tensorflow/core/util/sparse/sparse_tensor_test.cc tensorflow-1.8.0/tensorflow/core/util/sparse/sparse_tensor_test.cc +--- tensorflow-1.8.0.orig/tensorflow/core/util/sparse/sparse_tensor_test.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/util/sparse/sparse_tensor_test.cc 2018-04-30 17:58:54.216085602 +0200 +@@ -356,7 +356,7 @@ + Tensor dense(DT_STRING, TensorShape({4, 4, 5})); + st.ToDense(&dense); + +- auto dense_t = dense.tensor(); ++ auto dense_t = dense.template tensor(); + Eigen::array ix_n; + for (int n = 0; n < N; ++n) { + for (int d = 0; d < NDIM; ++d) ix_n[d] = ix_t(n, d); +@@ -395,7 +395,7 @@ + Tensor dense(DT_STRING, TensorShape({10, 10, 10})); + st.ToDense(&dense); + +- auto dense_t = dense.tensor(); ++ auto dense_t = dense.template tensor(); + Eigen::array ix_n; + for (int n = 0; n < N; ++n) { + for (int d = 0; d < NDIM; ++d) ix_n[d] = ix_t(n, d); +diff -ru tensorflow-1.8.0.orig/tensorflow/examples/ios/benchmark/BenchmarkViewController.mm tensorflow-1.8.0/tensorflow/examples/ios/benchmark/BenchmarkViewController.mm +--- tensorflow-1.8.0.orig/tensorflow/examples/ios/benchmark/BenchmarkViewController.mm 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/examples/ios/benchmark/BenchmarkViewController.mm 2018-04-30 17:59:03.800027420 +0200 +@@ -231,7 +231,7 @@ + tensorflow::DT_FLOAT, + tensorflow::TensorShape( + {1, wanted_height, wanted_width, wanted_channels})); +- auto image_tensor_mapped = image_tensor.tensor(); ++ auto image_tensor_mapped = image_tensor.template tensor(); + tensorflow::uint8* in = image_data.data(); + float* out = image_tensor_mapped.data(); + for (int y = 0; y < wanted_height; ++y) { +diff -ru tensorflow-1.8.0.orig/tensorflow/examples/ios/camera/CameraExampleViewController.mm tensorflow-1.8.0/tensorflow/examples/ios/camera/CameraExampleViewController.mm +--- tensorflow-1.8.0.orig/tensorflow/examples/ios/camera/CameraExampleViewController.mm 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/examples/ios/camera/CameraExampleViewController.mm 2018-04-30 17:59:04.084025696 +0200 +@@ -293,7 +293,7 @@ + tensorflow::DT_FLOAT, + tensorflow::TensorShape( + {1, wanted_input_height, wanted_input_width, wanted_input_channels})); +- auto image_tensor_mapped = image_tensor.tensor(); ++ auto image_tensor_mapped = image_tensor.template tensor(); + tensorflow::uint8 *in = sourceStartAddr; + float *out = image_tensor_mapped.data(); + for (int y = 0; y < wanted_input_height; ++y) { +diff -ru tensorflow-1.8.0.orig/tensorflow/examples/ios/simple/RunModelViewController.mm tensorflow-1.8.0/tensorflow/examples/ios/simple/RunModelViewController.mm +--- tensorflow-1.8.0.orig/tensorflow/examples/ios/simple/RunModelViewController.mm 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/examples/ios/simple/RunModelViewController.mm 2018-04-30 17:59:04.492023219 +0200 +@@ -180,7 +180,7 @@ + tensorflow::DT_FLOAT, + tensorflow::TensorShape({ + 1, wanted_height, wanted_width, wanted_channels})); +- auto image_tensor_mapped = image_tensor.tensor(); ++ auto image_tensor_mapped = image_tensor.template tensor(); + tensorflow::uint8* in = image_data.data(); + // tensorflow::uint8* in_end = (in + (image_height * image_width * image_channels)); + float* out = image_tensor_mapped.data(); +diff -ru tensorflow-1.8.0.orig/tensorflow/tools/graph_transforms/flatten_atrous.cc tensorflow-1.8.0/tensorflow/tools/graph_transforms/flatten_atrous.cc +--- tensorflow-1.8.0.orig/tensorflow/tools/graph_transforms/flatten_atrous.cc 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/tools/graph_transforms/flatten_atrous.cc 2018-04-30 18:00:06.007650099 +0200 +@@ -81,8 +81,8 @@ + TensorShape({upsampled_filter_height, upsampled_filter_width, + in_channels, out_channels})); + +- auto filter_eigen = filter.tensor(); +- auto upsampled_filter_eigen = upsampled_filter.tensor(); ++ auto filter_eigen = filter.template tensor(); ++ auto upsampled_filter_eigen = upsampled_filter.template tensor(); + + upsampled_filter_eigen.setZero(); + for (int h = 0; h < filter_height; ++h) { diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0_lrt-flag.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0_lrt-flag.patch new file mode 100644 index 00000000000..9098e97dbfd --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0_lrt-flag.patch @@ -0,0 +1,32 @@ +# Required on CentOS6 +# https://github.com/tensorflow/tensorflow/issues/15129 +--- tensorflow/tensorflow.bzl.old 2018-03-28 13:36:45.640203970 +0200 ++++ tensorflow/tensorflow.bzl 2018-03-28 13:37:17.867282309 +0200 +@@ -283,7 +283,7 @@ + name, + srcs=[], + deps=[], +- linkopts=[], ++ linkopts=["-lrt"], + framework_so=tf_binary_additional_srcs(), + **kwargs): + native.cc_binary( +@@ -1292,7 +1292,7 @@ + ) + + def tf_extension_linkopts(): +- return [] # No extension link opts ++ return ["-lrt"] # No extension link opts + + def tf_extension_copts(): + return [] # No extension c opts +--- tensorflow/contrib/lite/toco/BUILD.orig 2018-05-02 13:39:29.902538000 +0800 ++++ tensorflow/contrib/lite/toco/BUILD 2018-05-02 13:40:01.429545282 +0800 +@@ -409,6 +409,7 @@ + "//tensorflow/core:lib", + "@com_google_absl//absl/strings", + ], ++ linkopts = ["-lrt"], + ) + + tf_cc_test( diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0_no_boringssl.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0_no_boringssl.patch new file mode 100644 index 00000000000..fb037b9a0c8 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0_no_boringssl.patch @@ -0,0 +1,104 @@ +# Disable boringssl which fails to build due to incorrect C code with +# Intel compiler +# +# Åke Sandgren, HPC2N +diff -ru tensorflow-1.8.0-rc1.orig/tensorflow/core/platform/cloud/BUILD tensorflow-1.8.0-rc1/tensorflow/core/platform/cloud/BUILD +--- tensorflow-1.8.0-rc1.orig/tensorflow/core/platform/cloud/BUILD 2018-04-19 17:53:13.000000000 +0200 ++++ tensorflow-1.8.0-rc1/tensorflow/core/platform/cloud/BUILD 2018-04-24 20:22:00.361149553 +0200 +@@ -179,7 +179,6 @@ + ":http_request", + "//tensorflow/core:lib", + "//tensorflow/core:lib_internal", +- "@boringssl//:crypto", + "@jsoncpp_git//:jsoncpp", + ], + ) +@@ -323,7 +322,6 @@ + "//tensorflow/core:lib_internal", + "//tensorflow/core:test", + "//tensorflow/core:test_main", +- "@boringssl//:crypto", + ], + ) + +diff -ru tensorflow-1.8.0-rc1.orig/tensorflow/core/platform/s3/BUILD tensorflow-1.8.0-rc1/tensorflow/core/platform/s3/BUILD +--- tensorflow-1.8.0-rc1.orig/tensorflow/core/platform/s3/BUILD 2018-04-19 17:53:13.000000000 +0200 ++++ tensorflow-1.8.0-rc1/tensorflow/core/platform/s3/BUILD 2018-04-24 20:22:07.981104387 +0200 +@@ -51,7 +51,6 @@ + "//tensorflow/core:lib", + "//tensorflow/core:lib_internal", + "@aws", +- "@boringssl//:crypto", + ], + alwayslink = 1, + ) +diff -ru tensorflow-1.8.0-rc1.orig/tensorflow/tools/lib_package/BUILD tensorflow-1.8.0-rc1/tensorflow/tools/lib_package/BUILD +--- tensorflow-1.8.0-rc1.orig/tensorflow/tools/lib_package/BUILD 2018-04-19 17:53:13.000000000 +0200 ++++ tensorflow-1.8.0-rc1/tensorflow/tools/lib_package/BUILD 2018-04-24 20:22:13.257073119 +0200 +@@ -114,7 +114,6 @@ + "//third_party/eigen3:LICENSE", + "//third_party/fft2d:LICENSE", + "@aws//:LICENSE", +- "@boringssl//:LICENSE", + "@com_googlesource_code_re2//:LICENSE", + "@cub_archive//:LICENSE.TXT", + "@curl//:COPYING", +@@ -151,7 +150,6 @@ + "//third_party/eigen3:LICENSE", + "//third_party/fft2d:LICENSE", + "@aws//:LICENSE", +- "@boringssl//:LICENSE", + "@com_googlesource_code_re2//:LICENSE", + "@cub_archive//:LICENSE.TXT", + "@curl//:COPYING", +diff -ru tensorflow-1.8.0-rc1.orig/tensorflow/tools/pip_package/BUILD tensorflow-1.8.0-rc1/tensorflow/tools/pip_package/BUILD +--- tensorflow-1.8.0-rc1.orig/tensorflow/tools/pip_package/BUILD 2018-04-19 17:53:13.000000000 +0200 ++++ tensorflow-1.8.0-rc1/tensorflow/tools/pip_package/BUILD 2018-04-24 20:22:17.333048966 +0200 +@@ -124,7 +124,6 @@ + "@arm_neon_2_x86_sse//:LICENSE", + "@astor_archive//:LICENSE", + "@aws//:LICENSE", +- "@boringssl//:LICENSE", + "@com_google_absl//:LICENSE", + "@com_googlesource_code_re2//:LICENSE", + "@cub_archive//:LICENSE.TXT", +diff -ru tensorflow-1.8.0-rc1.orig/tensorflow/workspace.bzl tensorflow-1.8.0-rc1/tensorflow/workspace.bzl +--- tensorflow-1.8.0-rc1.orig/tensorflow/workspace.bzl 2018-04-19 17:53:13.000000000 +0200 ++++ tensorflow-1.8.0-rc1/tensorflow/workspace.bzl 2018-04-24 20:22:36.208937145 +0200 +@@ -766,12 +766,6 @@ + + # Needed by gRPC + native.bind( +- name = "libssl", +- actual = "@boringssl//:ssl", +- ) +- +- # Needed by gRPC +- native.bind( + name = "nanopb", + actual = "@grpc//third_party/nanopb:nanopb", + ) +diff -ru tensorflow-1.8.0-rc1.orig/third_party/curl.BUILD tensorflow-1.8.0-rc1/third_party/curl.BUILD +--- tensorflow-1.8.0-rc1.orig/third_party/curl.BUILD 2018-04-19 17:53:13.000000000 +0200 ++++ tensorflow-1.8.0-rc1/third_party/curl.BUILD 2018-04-24 20:23:05.812761875 +0200 +@@ -315,9 +315,6 @@ + "@org_tensorflow//tensorflow:ios": [], + "@org_tensorflow//tensorflow:windows": [], + "@org_tensorflow//tensorflow:windows_msvc": [], +- "//conditions:default": [ +- "@boringssl//:ssl", +- ], + }), + ) + +diff -ru tensorflow-1.8.0-rc1.orig/third_party/kafka/BUILD tensorflow-1.8.0-rc1/third_party/kafka/BUILD +--- tensorflow-1.8.0-rc1.orig/third_party/kafka/BUILD 2018-04-19 17:53:13.000000000 +0200 ++++ tensorflow-1.8.0-rc1/third_party/kafka/BUILD 2018-04-24 20:23:13.224718012 +0200 +@@ -146,7 +146,6 @@ + ], + visibility = ["//visibility:public"], + deps = [ +- "@boringssl//:ssl", + "@zlib_archive//:zlib", + ], + ) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0_no_grpc.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0_no_grpc.patch new file mode 100644 index 00000000000..60b6c426aeb --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0_no_grpc.patch @@ -0,0 +1,16 @@ +# Disable GRPC_SUPPORT, it depends on boringssl, which fails to build +# with Intel +# +# Åke Sandgren, HPC2N +diff -ru tensorflow-1.8.0-rc1.orig/tensorflow/contrib/cmake/CMakeLists.txt tensorflow-1.8.0-rc1/tensorflow/contrib/cmake/CMakeLists.txt +--- tensorflow-1.8.0-rc1.orig/tensorflow/contrib/cmake/CMakeLists.txt 2018-04-19 17:53:13.000000000 +0200 ++++ tensorflow-1.8.0-rc1/tensorflow/contrib/cmake/CMakeLists.txt 2018-04-24 20:13:42.480033417 +0200 +@@ -19,7 +19,7 @@ + # Options + option(tensorflow_VERBOSE "Enable for verbose output" OFF) + option(tensorflow_ENABLE_SSL_SUPPORT "Enable boringssl support" OFF) +-option(tensorflow_ENABLE_GRPC_SUPPORT "Enable gRPC support" ON) ++option(tensorflow_ENABLE_GRPC_SUPPORT "Enable gRPC support" OFF) + option(tensorflow_ENABLE_HDFS_SUPPORT "Enable HDFS support" OFF) + option(tensorflow_ENABLE_JEMALLOC_SUPPORT "Enable jemalloc support" OFF) + option(tensorflow_BUILD_CC_EXAMPLE "Build the C++ tutorial example" ON) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0_remove-msse-hardcoding.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0_remove-msse-hardcoding.patch new file mode 100644 index 00000000000..05bb43b4108 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0_remove-msse-hardcoding.patch @@ -0,0 +1,28 @@ +remove hardcoding of -msse4.2 since it overrules -xHost when using Intel compilers +author: Kenneth Hoste (HPC-UGent) +--- tensorflow-1.8.0/tensorflow/core/BUILD.orig 2018-04-27 18:36:49.000000000 +0200 ++++ tensorflow-1.8.0/tensorflow/core/BUILD 2018-04-30 10:14:18.578951874 +0200 +@@ -1755,7 +1755,7 @@ + name = "lib_hash_crc32c_accelerate_internal", + srcs = ["lib/hash/crc32c_accelerate.cc"], + # -msse4.2 enables the use of crc32c compiler builtins. +- copts = tf_copts() + if_linux_x86_64(["-msse4.2"]), ++ copts = tf_copts() + if_linux_x86_64([""]), + ) + + cc_library( +--- tensorflow-1.8.0/tensorflow/tensorflow.bzl.orig 2018-04-30 10:14:18.578951874 +0200 ++++ tensorflow-1.8.0/tensorflow/tensorflow.bzl 2018-04-30 10:18:11.170269763 +0200 +@@ -205,9 +205,9 @@ + + if_tensorrt(["-DGOOGLE_TENSORRT=1"]) + + if_mkl(["-DINTEL_MKL=1", "-DEIGEN_USE_VML"]) + + if_mkl_lnx_x64(["-fopenmp"]) +- + if_android_arm(["-mfpu=neon"]) +- + if_linux_x86_64(["-msse3"]) +- + if_ios_x86_64(["-msse4.1"]) ++ + if_android_arm([""]) ++ + if_linux_x86_64([""]) ++ + if_ios_x86_64([""]) + + select({ + clean_dep("//tensorflow:framework_shared_object"): [], + "//conditions:default": ["-DTENSORFLOW_MONOLITHIC_BUILD"], diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-6.4.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..ca41e4d22a9 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-6.4.0.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.20.00' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b89de7064ab54dac454a266cfe5d8bf66940cb5ed048d0c30674ea62e7ecef9d'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.26', '', True)] + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.25-foss-2017b.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.25-foss-2017b.eb new file mode 100644 index 00000000000..dc2f44415bd --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.25-foss-2017b.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.2.25' + +homepage = 'http://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.unidata.ucar.edu/pub/udunits'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ad486f8f45cba915ac74a38dd15f96a661a1803287373639c17e5a9b59bfd540'] + +dependencies = [('expat', '2.2.4')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.32-GCCcore-6.4.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.32-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..3de7b38ced4 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.32-GCCcore-6.4.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.32' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' + +description = "Set of Linux utilities" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ce43afee3182f1bddb0be83f68bd378770efb9b6fdd8f464333ff8e07903db56'] + +# disable account related utilities (they need OS dependent pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su --disable-rfkill " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.15-foss-2018a-Perl-5.26.1.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.15-foss-2018a-Perl-5.26.1.eb new file mode 100644 index 00000000000..3d0b4f9d807 --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.15-foss-2018a-Perl-5.26.1.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'VCFtools' +version = '0.1.15' +versionsuffix = '-Perl-%(perlver)s' + +homepage = "https://vcftools.github.io" +description = """The aim of VCFtools is to provide + easily accessible methods for working with complex + genetic variation data in the form of VCF files.""" + +toolchain = {'name': 'foss', 'version': '2018a'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['31e47afd5be679d89ece811a227525925b6907cce4af2c86f10f465e080383e3'] + +dependencies = [ + ('Perl', '5.26.1'), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['vcftools', 'vcf-sort', 'vcf-stats']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VTune/VTune-2018_update2.eb b/easybuild/easyconfigs/v/VTune/VTune-2018_update2.eb new file mode 100644 index 00000000000..6121c0cc647 --- /dev/null +++ b/easybuild/easyconfigs/v/VTune/VTune-2018_update2.eb @@ -0,0 +1,19 @@ +name = 'VTune' +version = '2018_update2' + +homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' +description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, + Assembly and Java.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['vtune_amplifier_%(version)s.tar.gz'] +checksums = ['5b21dd0c598e7e8a80be7095e13869a746c5074fa030211ca698ae2cfc65da93'] + +license_file = HOME + '/licenses/intel/license.lic' +# +# Use this configuration to use a license server: +# license_file = '12345@license.example.com' +# + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-17.1-foss-2018a.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-17.1-foss-2018a.eb new file mode 100644 index 00000000000..330e1c5cc0a --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-17.1-foss-2018a.eb @@ -0,0 +1,44 @@ +name = 'WIEN2k' +version = '17.1' + +homepage = 'http://www.wien2k.at/' +description = """The program package WIEN2k allows to perform electronic structure calculations of solids +using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave +((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. +WIEN2k is an all-electron scheme including relativistic effects and has many features.""" + +toolchain = {'name': 'foss', 'version': '2018a'} + +sources = ['%(name)s_%(version)s.tar'] +checksums = ['4475410e16289edca416405cebbf51c63113ceee28aa5e2df356f1225cb260d7'] + +dependencies = [ + ('ELPA', '2015.02.002'), + ('FFTW', '3.3.7'), + ('libxc', '3.0.1'), +] + +osdependencies = ['glib-devel'] # required for libpthread.a + +remote = 'pbsssh' +wien_mpirun = 'mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_' +use_remote = True +mpi_remote = False +wien_granularity = True +taskset = 'no' + +tests = [ + # test case 1: NaCl + ('NaCl', '-b', '-i 3', [r'^:DIS.*0.122[67]', r'^:ENE.*-1248.142[56]']), + # test case 2: TiO2 + ('TiO2', + '-b -numk 1000 -rkmax 7.5', + '-in1ef -cc 0.00001 -fc 0.5 -i 100', + [ + r'^:ENE.*-4018.07', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*14.70.*total forces', + ]), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-17.1-gimkl-2017a.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-17.1-gimkl-2017a.eb new file mode 100644 index 00000000000..c67d7f46955 --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-17.1-gimkl-2017a.eb @@ -0,0 +1,44 @@ +name = 'WIEN2k' +version = '17.1' + +homepage = 'http://www.wien2k.at/' +description = """The program package WIEN2k allows to perform electronic structure calculations of solids +using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave +((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. +WIEN2k is an all-electron scheme including relativistic effects and has many features.""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} + +sources = ['%(name)s_%(version)s.tar'] +checksums = ['4475410e16289edca416405cebbf51c63113ceee28aa5e2df356f1225cb260d7'] + +dependencies = [ + ('ELPA', '2015.02.002'), + ('FFTW', '3.3.7'), + ('libxc', '3.0.1'), +] + +osdependencies = ['glib-devel'] # required for libpthread.a + +remote = 'pbsssh' +wien_mpirun = 'mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_' +use_remote = True +mpi_remote = False +wien_granularity = True +taskset = 'no' + +tests = [ + # test case 1: NaCl + ('NaCl', '-b', '-i 3', [r'^:DIS.*0.122[67]', r'^:ENE.*-1248.142[56]']), + # test case 2: TiO2 + ('TiO2', + '-b -numk 1000 -rkmax 7.5', + '-in1ef -cc 0.00001 -fc 0.5 -i 100', + [ + r'^:ENE.*-4018.07', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*14.70.*total forces', + ]), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-17.1-intel-2018a.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-17.1-intel-2018a.eb new file mode 100644 index 00000000000..75b605ea618 --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-17.1-intel-2018a.eb @@ -0,0 +1,44 @@ +name = 'WIEN2k' +version = '17.1' + +homepage = 'http://www.wien2k.at/' +description = """The program package WIEN2k allows to perform electronic structure calculations of solids +using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave +((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. +WIEN2k is an all-electron scheme including relativistic effects and has many features.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +sources = ['%(name)s_%(version)s.tar'] +checksums = ['4475410e16289edca416405cebbf51c63113ceee28aa5e2df356f1225cb260d7'] + +dependencies = [ + ('ELPA', '2015.02.002'), + ('FFTW', '3.3.7'), + ('libxc', '3.0.1'), +] + +osdependencies = ['glib-devel'] # required for libpthread.a + +remote = 'pbsssh' +wien_mpirun = 'mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_' +use_remote = True +mpi_remote = False +wien_granularity = True +taskset = 'no' + +tests = [ + # test case 1: NaCl + ('NaCl', '-b', '-i 3', [r'^:DIS.*0.122[67]', r'^:ENE.*-1248.142[56]']), + # test case 2: TiO2 + ('TiO2', + '-b -numk 1000 -rkmax 7.5', + '-in1ef -cc 0.00001 -fc 0.5 -i 100', + [ + r'^:ENE.*-4018.07', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*14.70.*total forces', + ]), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.31.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/w/wheel/wheel-0.31.0-foss-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..8b9b07f21a2 --- /dev/null +++ b/easybuild/easyconfigs/w/wheel/wheel-0.31.0-foss-2018a-Python-3.6.4.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'wheel' +version = '0.31.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/wheel' +description = """A built-package format for Python.""" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['1ae8153bed701cb062913b72429bcf854ba824f973735427681882a688cb55ce'] + +dependencies = [('Python', '3.6.4')] + +sanity_check_paths = { + 'files': ['bin/wheel'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.0.3-foss-2018a.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.0.3-foss-2018a.eb new file mode 100644 index 00000000000..63a4407592f --- /dev/null +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.0.3-foss-2018a.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'wxWidgets' +version = '3.0.3' + +homepage = 'https://www.wxwidgets.org' +description = """ wxWidgets is a C++ library that lets developers create applications + for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular + language bindings for Python, Perl, Ruby and many other languages, and unlike other + cross-platform toolkits, wxWidgets gives applications a truly native look and feel + because it uses the platform's native API rather than emulating the GUI. """ + +toolchain = {'name': 'foss', 'version': '2018a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/wxWidgets/wxWidgets/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1ec3655765c33ad5f5fe2a7a028a13dbf20c350b97a4fe47c7d45c4a7d976042'] + +dependencies = [ + ('libpng', '1.6.34'), + ('zlib', '1.2.11'), + ('libjpeg-turbo', '1.5.3'), + ('LibTIFF', '4.0.9'), + ('expat', '2.2.5'), + ('GTK+', '2.24.32'), + ('Mesa', '17.3.6'), + ('libGLU', '9.0.0'), +] + +configopts = '--with-opengl' + +sanity_check_paths = { + 'files': ['bin/wx-config', 'bin/wxrc'], + 'dirs': ['include/wx-3.0/wx', 'lib', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0132-GCCcore-6.4.0-Perl-5.26.1.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0132-GCCcore-6.4.0-Perl-5.26.1.eb new file mode 100644 index 00000000000..decbc41f04f --- /dev/null +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0132-GCCcore-6.4.0-Perl-5.26.1.eb @@ -0,0 +1,33 @@ +easyblock = 'PerlModule' + +name = 'XML-LibXML' +version = '2.0132' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://search.cpan.org/src/SHLOMIF/XML-LibXML-2.0018/' +description = """Perl binding for libxml2""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'] +sources = [SOURCE_TAR_GZ] +patches = ['XML-LibXML-%(version)s_fix-02parse-test.patch'] +checksums = [ + '721452e3103ca188f5968ab06d5ba29fe8e00e49f4767790882095050312d476', # XML-LibXML-2.0132.tar.gz + '6f27d43b1f84427791fa035fbce2fbedd73f9a0bfacdba1a557477a7844322d5', # XML-LibXML-2.0132_fix-02parse-test.patch +] + +builddependencies = [('binutils', '2.28')] +dependencies = [ + ('Perl', '5.26.1'), + ('libxml2', '2.9.7'), +] + +options = {'modulename': 'XML::LibXML'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML/LibXML'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.10.3-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/x/xarray/xarray-0.10.3-intel-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..b6f7a2d47bd --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-0.10.3-intel-2018a-Python-3.6.4.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'xarray' +version = '0.10.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['72fafe29ba00633483aed39e405442226ef66d2ddc1021a39527ae1522b7067a'] + +dependencies = [('Python', '3.6.4')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.10.4-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/x/xarray/xarray-0.10.4-intel-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..0fcfb30be90 --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-0.10.4-intel-2018a-Python-3.6.4.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'xarray' +version = '0.10.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['64c2d07b75b8ea1320cba521818a2f09107f5f46514d50ff5ef1c4d5da90aaf1'] + +dependencies = [('Python', '3.6.4')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.5-foss-2018a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.5-foss-2018a.eb new file mode 100644 index 00000000000..95dc0b6cb99 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.5-foss-2018a.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.2.5' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cc9090ba35713d59bb2f7d7965f877036c49c5558ea0c290b0dcc6f2a17e489f'] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.31.1'), + ('libsodium', '1.0.16'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.1.0.eb new file mode 100644 index 00000000000..f97c6752989 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.1.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.11' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '8.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.30', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/setup.py b/setup.py index 7eff38a1b00..02848476725 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.6.0' +VERSION = '3.6.1' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2])