Merge pull request easybuilders#6577 from easybuilders/3.6.x

release EasyBuild v3.6.2
bartoldeman · Jul 11, 2018 · afb3447 · afb3447
2 parents 96d4f78 + 248bc1f
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diff --git a/RELEASE_NOTES b/RELEASE_NOTES
@@ -3,9 +3,51 @@ 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 8,983 easyconfig files, for 1,461 different software packages,
+The latest version of easybuild-easyconfig provides 9,247 easyconfig files, for 1,489 different software packages,
 30 different (compiler) toolchains, 13 software bundles and 1 meta-package.
 
+v3.6.2 (July 11th 2018)
+-----------------------
+
+bugfix/update release
+- added easyconfigs for new toolchains: foss/2018b (#6424), fosscuda/2018b (#6555) and intel/2018b (#6409)
+- added example easyconfig files for 28 new software packages:
+  - CUnit (#6469), eggnog-mapper (#6513), FANN (#6468), FTGL (#6421), FreeFem++ (#5918), fastStructure (#6448),
+    fastq-tools (#5396), fullrmc (#6422), GDGraph (#6529), heaptrack (#6450), libgpuarray (#5429), lz4 (#6449),
+    MAJIQ (#5983), makedepf90 (#6504), nanopolish (#6464), opencv_contrib (#6441), PRC (#6477), Pillow-SIMD (#6152),
+    Pytorch (#6152), poretools (#6467), pystran (#6395), R-keras (#6530), Scoary (#6521), Scrappie (#6469),
+    torchvision (#6152), WISExome (#6524), WannierTools (#6539), zstd (#6449, #6452)
+- added additional easyconfigs for various supported software packages, including:
+  - GROMACS 2018.2, HDF5 1.10.2, IPython 6.3.1, Kraken 1.0, Mesa 18.1.1, netCDF 4.6.1, NWChem 6.8, OpenBLAS 0.3.1,
+    OpenMPI 3.1.1, Perl 5.28.0, Python 2.7.15, R 3.5.0, X11 20180604
+- minor enhancements, including:
+  - add hint on file name differences between downloaded and expected in cuDNN easyconfig (#6042)
+  - add 'gee' extension to R 3.4.4 easyconfigs (#6376)
+  - enable building of MPI libraries in VTK 8.1.0 easyconfigs (#6460, #6429)
+- minor changes, including:
+  - rename 'Canu' to 'canu' for v1.7 (#6389)
+  - update existing easyconfigs for OpenCV 3.4.1 to use new custom easyblock for OpenCV (#6509) 
+  - fix software name in Bsoft easyconfig (#6557)
+- various bug fixes, including:
+  - fix SAMtools dependency for ChimPipe, required SAMtools < 1.0 (#5930)
+  - skip installing of documentation in easyconfig for jemalloc 5.0.1 (#6428)
+  - stop including GCCcore 6.4.0 as build dep for GCCcore 8.1.0 (#6431)
+    - no longer needed with updated GCC easyblock
+  - add patch for GCCcore 6.4.0 to fix compilation problems on glibc 2.26 systems (#6432, #6495)
+  - fix checksums for pkgmaker/rngtools/RWeka/RcppProgress/mgcv extensions in R 3.4.4 easyconfigs (#6446, #6502)
+  - added necessary compiler flag for Guile 1.8.8 (#6457)
+  - build hwloc 1.11.10 with -fno-tree-vectorize to avoid segfaulting lstopo on Intel Skylake (#6461)
+  - add patch for binutils 2.30 to fix assertion failure (#6463)
+  - sync extensions in Python-3.6.4-iomkl-2018a.eb easyconfig with other Python 3.6.4 easyconfigs using 2018a toolchain (#6471)
+  - enable checking/setting of unlimited stack limit in Python 3.6.x easyconfigs using an 'intel' toolchain (#6485, #6492)
+  - add missing libxml2 dependency for HDF5 1.10.1 (#6498)
+  - also copy eggnog-mapper scripts (#6522)
+  - fix missing dependencies for Perl modules included as extensions for Perl 5.26.1 (#6532) and 5.28.0 (#6533)
+  - fix location of include directory in libffi 3.2.1 easyconfigs (#6565)
+- other changes
+  - also check for multiple dependency variants in easyconfigs using GCCcore 7.3.0 & newer (#6444)
+
+
 v3.6.1 (May 28th 2018)
 ----------------------
 

diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018a-Python-2.7.14.eb
@@ -0,0 +1,35 @@
+easyblock = 'ConfigureMake'
+
+name = 'ANTLR'
+version = '2.7.7'
+versionsuffix = '-Python-%(pyver)s'
+
+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': '2018a'}
+
+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_162', '', True),
+    ('Python', '2.7.14'),
+]
+
+configopts = '--disable-examples --disable-csharp '
+
+sanity_check_paths = {
+    'files': ['bin/antlr', 'bin/antlr-config'],
+    'dirs': ['include'],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.16.2-iomkl-2018.02-Python-3.6.4.eb b/easybuild/easyconfigs/a/ASE/ASE-3.16.2-iomkl-2018.02-Python-3.6.4.eb
@@ -0,0 +1,31 @@
+easyblock = 'PythonPackage'
+
+name = 'ASE'
+version = '3.16.2'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'http://wiki.fysik.dtu.dk/ase'
+description = """ASE is a python package providing an open source Atomic Simulation Environment
+ in the Python scripting language."""
+
+toolchain = {'name': 'iomkl', 'version': '2018.02'}
+
+source_urls = [PYPI_LOWER_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['5e63e7dc18fd13dcc3cb46ab3de019375b9d62c6c3a845a99f34b6928251f4c2']
+
+dependencies = [
+    ('Python', '3.6.4'),
+    ('Tkinter', '%(pyver)s', '-Python-%(pyver)s'),
+    ('matplotlib', '2.1.2', '-Python-%(pyver)s'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/ase'],
+    'dirs': [],
+}
+
+# make sure Tkinter is available, otherwise 'ase gui' will not work
+sanity_check_commands = ["python -c 'import tkinter' "]
+
+moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.16.2-iomkl-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/a/ASE/ASE-3.16.2-iomkl-2018a-Python-3.6.4.eb
@@ -0,0 +1,31 @@
+easyblock = 'PythonPackage'
+
+name = 'ASE'
+version = '3.16.2'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'http://wiki.fysik.dtu.dk/ase'
+description = """ASE is a python package providing an open source Atomic Simulation Environment
+ in the Python scripting language."""
+
+toolchain = {'name': 'iomkl', 'version': '2018a'}
+
+source_urls = [PYPI_LOWER_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['5e63e7dc18fd13dcc3cb46ab3de019375b9d62c6c3a845a99f34b6928251f4c2']
+
+dependencies = [
+    ('Python', '3.6.4'),
+    ('Tkinter', '%(pyver)s', '-Python-%(pyver)s'),
+    ('matplotlib', '2.1.2', '-Python-%(pyver)s'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/ase'],
+    'dirs': [],
+}
+
+# make sure Tkinter is available, otherwise 'ase gui' will not work
+sanity_check_commands = ["python -c 'import tkinter' "]
+
+moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.27.1-intel-2017b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.27.1-intel-2017b.eb
@@ -0,0 +1,34 @@
+easyblock = 'ConfigureMake'
+
+name = 'ATK'
+version = '2.27.1'
+
+homepage = 'https://developer.gnome.org/ATK/stable/'
+description = """
+ ATK provides the set of accessibility interfaces that are implemented by other
+ toolkits and applications. Using the ATK interfaces, accessibility tools have
+ full access to view and control running applications.
+"""
+
+toolchain = {'name': 'intel', 'version': '2017b'}
+
+source_urls = [FTPGNOME_SOURCE]
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['673a953987b301ab1e24e7d11677b6e7ba3226411a168449ba946765b6d44297']
+
+builddependencies = [('GObject-Introspection', '1.53.5', '-Python-2.7.14')]
+
+dependencies = [('GLib', '2.53.5')]
+
+configopts = "--enable-introspection=yes"
+
+modextrapaths = {
+    'XDG_DATA_DIRS': 'share',
+}
+
+sanity_check_paths = {
+    'files': ['lib/libatk-1.0.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.28.1-intel-2018a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.28.1-intel-2018a.eb
@@ -0,0 +1,37 @@
+easyblock = 'ConfigureMake'
+
+name = 'ATK'
+version = '2.28.1'
+
+homepage = 'https://developer.gnome.org/ATK/stable/'
+description = """
+ ATK provides the set of accessibility interfaces that are implemented by other
+ toolkits and applications. Using the ATK interfaces, accessibility tools have
+ full access to view and control running applications.
+"""
+
+toolchain = {'name': 'intel', 'version': '2018a'}
+
+source_urls = [FTPGNOME_SOURCE]
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['cd3a1ea6ecc268a2497f0cd018e970860de24a6d42086919d6bf6c8e8d53f4fc']
+
+builddependencies = [
+    ('GObject-Introspection', '1.54.1', '-Python-2.7.14'),
+]
+dependencies = [
+    ('GLib', '2.54.3'),
+]
+
+configopts = "--enable-introspection=yes"
+
+modextrapaths = {
+    'XDG_DATA_DIRS': 'share',
+}
+
+sanity_check_paths = {
+    'files': ['lib/libatk-1.0.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-7.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-7.3.0.eb
@@ -0,0 +1,38 @@
+easyblock = 'ConfigureMake'
+
+name = 'Autoconf'
+version = '2.69'
+
+homepage = 'http://www.gnu.org/software/autoconf/'
+
+description = """
+ Autoconf is an extensible package of M4 macros that produce shell scripts
+ to automatically configure software source code packages. These scripts can
+ adapt the packages to many kinds of UNIX-like systems without manual user
+ intervention. Autoconf creates a configuration script for a package from a
+ template file that lists the operating system features that the package can
+ use, in the form of M4 macro calls.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '7.3.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969']
+
+builddependencies = [
+    ('binutils', '2.30'),
+]
+
+dependencies = [
+    ('M4', '1.4.18'),
+]
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x
+              for x in ["autoconf", "autoheader", "autom4te", "autoreconf",
+                        "autoscan", "autoupdate", "ifnames"]],
+    'dirs': [],
+}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-7.3.0.eb
@@ -0,0 +1,41 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
+# Authors::   Fotis Georgatos <[email protected]>
+# 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/
+##
+
+easyblock = 'ConfigureMake'
+
+name = 'Automake'
+version = '1.16.1'
+
+homepage = 'http://www.gnu.org/software/automake/automake.html'
+
+description = "Automake: GNU Standards-compliant Makefile generator"
+
+toolchain = {'name': 'GCCcore', 'version': '7.3.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['608a97523f97db32f1f5d5615c98ca69326ced2054c9f82e65bade7fc4c9dea8']
+
+builddependencies = [
+    ('binutils', '2.30'),
+]
+
+dependencies = [
+    ('Autoconf', '2.69'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/automake', 'bin/aclocal'],
+    'dirs': []
+}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20180311-GCCcore-7.3.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20180311-GCCcore-7.3.0.eb
@@ -0,0 +1,24 @@
+easyblock = 'Bundle'
+
+name = 'Autotools'
+version = '20180311'  # 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': 'GCCcore', 'version': '7.3.0'}
+
+dependencies = [
+    ('Autoconf', '2.69'),    # 20120424
+    ('Automake', '1.16.1'),  # 20180311
+    ('libtool', '2.4.6'),    # 20150215
+]
+
+# Pure bundle -- no need to specify 'binutils' used when building GCCcore
+# toolchain as build dependency
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/a/angsd/angsd-0.921-foss-2018a.eb b/easybuild/easyconfigs/a/angsd/angsd-0.921-foss-2018a.eb
@@ -0,0 +1,27 @@
+easyblock = 'MakeCp'
+
+name = 'angsd'
+version = '0.921'
+
+homepage = 'http://www.popgen.dk/angsd'
+description = """Program for analysing NGS data."""
+
+toolchain = {'name': 'foss', 'version': '2018a'}
+
+source_urls = ['https://github.com/ANGSD/angsd/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['8892d279ce1804f9e17fe2fc65a47e5498e78fc1c1cb84d2ca2527fd5c198772']
+
+dependencies = [('HTSlib', '1.8')]
+
+files_to_copy = [
+    (['angsd'], 'bin'),
+    'doc',
+]
+
+sanity_check_paths = {
+    'files': ['bin/angsd'],
+    'dirs': ['doc'],
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-intel-2018a.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-intel-2018a.eb
@@ -0,0 +1,28 @@
+# 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
+# Modified by: Adam Huffman
+# The Francis Crick Institute
+
+easyblock = 'ConfigureMake'
+
+name = 'argtable'
+version = '2.13'
+
+homepage = 'http://argtable.sourceforge.net/'
+description = """ Argtable is an ANSI C library for parsing GNU style
+ command line options with a minimum of fuss. """
+
+toolchain = {'name': 'intel', 'version': '2018a'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['%s%s.tar.gz' % (name, version.replace('.', '-'))]
+checksums = ['8f77e8a7ced5301af6e22f47302fdbc3b1ff41f2b83c43c77ae5ca041771ddbf']
+
+sanity_check_paths = {
+    'files': ['lib/libargtable2.%s' % SHLIB_EXT, 'lib/libargtable2.la'],
+    'dirs': ['include', 'lib', 'share'],
+}
+
+moduleclass = 'lib'