From 9c68f9d2cd55113f47587a7aef98f1a148606e62 Mon Sep 17 00:00:00 2001 From: Keith James Date: Wed, 26 Sep 2018 08:59:24 +0100 Subject: [PATCH 001/119] Added a script to update our Conda channels when pre-built packages are dropped in the appropriate directory. --- .gitattributes | 1 + scripts/update_conda_channel.sh | 258 ++++++++++++++++++++++++ tests/data/packages/bar-1.0.0-0.tar.bz2 | Bin 0 -> 2286 bytes tests/data/packages/baz-1.0.0-0.tar.bz2 | Bin 0 -> 2287 bytes tests/data/packages/foo-1.0.0-0.tar.bz2 | Bin 0 -> 2294 bytes tests/data/recipes/bar/build.sh | 11 + tests/data/recipes/bar/meta.yaml | 17 ++ tests/data/recipes/baz/build.sh | 11 + tests/data/recipes/baz/meta.yaml | 17 ++ tests/data/recipes/foo/build.sh | 11 + tests/data/recipes/foo/meta.yaml | 17 ++ tests/run_tests.sh | 9 + tests/s3cmd | 50 +++++ tests/test_helper.bash | 36 ++++ tests/update_conda_channel.bats | 66 ++++++ 15 files changed, 504 insertions(+) create mode 100644 .gitattributes create mode 100755 scripts/update_conda_channel.sh create mode 100644 tests/data/packages/bar-1.0.0-0.tar.bz2 create mode 100644 tests/data/packages/baz-1.0.0-0.tar.bz2 create mode 100644 tests/data/packages/foo-1.0.0-0.tar.bz2 create mode 100644 tests/data/recipes/bar/build.sh create mode 100644 tests/data/recipes/bar/meta.yaml create mode 100644 tests/data/recipes/baz/build.sh create mode 100644 tests/data/recipes/baz/meta.yaml create mode 100644 tests/data/recipes/foo/build.sh create mode 100644 tests/data/recipes/foo/meta.yaml create mode 100755 tests/run_tests.sh create mode 100755 tests/s3cmd create mode 100644 tests/test_helper.bash create mode 100644 tests/update_conda_channel.bats diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 00000000..58c61c7a --- /dev/null +++ b/.gitattributes @@ -0,0 +1 @@ +*.bz2 -diff diff --git a/scripts/update_conda_channel.sh b/scripts/update_conda_channel.sh new file mode 100755 index 00000000..696ca11a --- /dev/null +++ b/scripts/update_conda_channel.sh @@ -0,0 +1,258 @@ +#!/bin/bash + +set -eo pipefail + +shopt -s nullglob + +trap cleanup EXIT INT TERM + +cleanup() { + if [ -d "$TMP_CHANNEL" ]; then + rm -r "$TMP_CHANNEL" + fi +} + +log_error() { + local msg="$1" + echo -e "$(print_iso8601_time)\tERROR\t$msg" +} + +log_notice() { + local msg="$1" + echo -e "$(print_iso8601_time)\tNOTICE\t$msg" +} + +print_iso8601_time() { + awk 'BEGIN { print strftime("%FT%T%z", systime()) }' +} + +usage() { + cat 1>&2 << EOF + +This script updates S3 Conda channels with any new packages that have +been placed in a local staging directory hierarchy. If any changes are +made to the remote channel, a copy of the previous state is preserved +on the local filesystem. + +The local directory hierarchy must be organised according to the +following conventions into roles ("prod", for production and "test", +for testing), Linux distributions ("Ubuntu", "RedHat"), releases +(e.g. "12.04", "16.04", "18.04" for Ubuntu, "7.5" for RedHat +Enterprise), and Conda software architecture (currently only +"linux-64"): + +Current state of deployed channels: + +/live/prod/RedHat/7.5/linux-64/ +/live/prod/Ubuntu/12.04/linux-64/ +/live/prod/Ubuntu/18.04/linux-64/ + +/live/test/RedHat/7.5/linux-64/ +/live/test/Ubuntu/12.04/linux-64/ +/live/test/Ubuntu/18.04/linux-64/ + +New packages to be deployed: + +/staging/test/Ubuntu/18.04/linux-64/* +/staging/prod/Ubuntu/18.04/linux-64/* + +Previous state of deployed channels: + +/archive/ + + +New packages should be added to the appropriate directories under +"staging" and this script run with the -r CLI option set to . This script will locate the new packages, move them into a copy +of the appropriate channel, index that channel and then synchronize it +to the S3 bucket and prefix. If that process is successful, the old +state of the channel under the "live" directory will be moved to a +timestamped directory in the "archive" directory and the new copy of +the channel will be moved to "live" to replace it. + +As this script will move file from staging, they must be given +suitable write permissions for the user running this script. + + +Usage: $0 -b -p -r + [-h] [-t ] [-v] [-y] + +Options: + + -b An existing S3 bucket name (without any s3:// prefix). Required. + + -h Print usage and exit. + + -p An S3 prefix within the bucket. Required. + + -r A local root directory containing Conda channels to be updated. + Required. + + -t The number of threads to use when indexing the channeld. Optional, + defaults to 8. + + -v Print verbose messages. + + -y Synchronise with S3 in dry-run mode (do nothing). Optional. + +EOF +} + + +S3CMD=s3cmd +S3_BUCKET= +S3_PREFIX= +S3_SYNC_ARGS=("--acl-public") + +NUM_THREADS=8 +LOCAL_ROOT= + +while getopts "b:hp:r:t:vy" option; do + case "$option" in + b) + S3_BUCKET="$OPTARG" + ;; + h) + usage + exit 0 + ;; + p) + S3_PREFIX="$OPTARG" + ;; + r) + LOCAL_ROOT="$OPTARG" + ;; + t) + NUM_THREADS="$OPTARG" + ;; + v) + set -x + ;; + y) + S3_SYNC_ARGS+=("--dry-run") + ;; + *) + usage + echo "Invalid argument!" + exit 4 + ;; + esac +done + +if [ -z "$S3_BUCKET" ] ; then + usage + echo -e "\nERROR:\n A -b argument is required" + exit 4 +fi + +if [ -z "$S3_PREFIX" ] ; then + usage + echo -e "\nERROR:\n A -p argument is required" + exit 4 +fi + +if [ -z "$LOCAL_ROOT" ] ; then + usage + echo -e "\nERROR:\n A -r argument is required" + exit 4 +fi + +if [ ! -d "$LOCAL_ROOT" ]; then + usage + echo -e "\nERROR:\n The local root directory '$LOCAL_ROOT' does not exist" + exit 4 +fi + +if [ "$NUM_THREADS" -ne "$NUM_THREADS" ]; then + usage + echo -e "\nERROR:\n The -t value must be an integer" + exit 4 +fi + +ARCHIVE_ROOT="$LOCAL_ROOT/archive" +LIVE_ROOT="$LOCAL_ROOT/live" +STAGING_ROOT="$LOCAL_ROOT/staging" + +CONDA_INDEX_ARGS=("--no-progress" "--threads" "$NUM_THREADS") +TMP_CHANNEL=$(mktemp -d ${TMPDIR:-/tmp/}$(basename -- "$0").XXXXXXXXXX) + +ROLES=("test" "prod") + +NUM_ERRORS=0 + +for role in "${ROLES[@]}"; do + log_notice "Working on $role ..." + distro_dirs=("$LIVE_ROOT/$role"/*) + + for distro_dir in "${distro_dirs[@]}"; do + distro=$(basename "$distro_dir") + log_notice "Working on $distro ..." + + release_dirs=("$distro_dir"/*) + for release_dir in "${release_dirs[@]}"; do + release=$(basename "$release_dir") + log_notice "Working on $release ..." + + now=$(print_iso8601_time) + release_dir="$LIVE_ROOT/$role/$distro/$release" + staging_dir="$STAGING_ROOT/$role/$distro/$release" + archive_dir="$ARCHIVE_ROOT/$role/$distro/$release/$now" + + # Find packages staged for addition to the channels + pkgs=("$staging_dir"/*/*.tar.bz2) + num_pkgs="${#pkgs[@]}" + if [ "$num_pkgs" -gt 0 ]; then + log_notice "Found $num_pkgs new packages staged in $staging_dir" + + # Create a temporary directory containing a copy of + # the current channel contents + tmp_dir=$(mktemp -d ${TMPDIR:-/tmp/}$(basename -- "$0").XXXXXXXXXX) + upload_dir="$tmp_dir/$role/$distro/$release" + mkdir -p "$upload_dir" + cp -r --no-target-directory "$release_dir" "$upload_dir" + + # Move staged packages to the temporary directory + for pkg in "${pkgs[@]}"; do + if [ ! -w "$pkg" ]; then + user=$(id -u -n) + log_error "$pkg is not writable by $user, skipping it" + (( NUM_ERRORS++ )) + fi + + architecture_dir=$(basename $(dirname "$pkg")) + mkdir -p "$upload_dir/$architecture_dir" + mv "$pkg" "$upload_dir/$architecture_dir" + done + + # Index the temporary directory as a Conda channel and + # upload to S3 + log_notice "Indexing $upload_dir" + conda index ${CONDA_INDEX_ARGS[@]} "$upload_dir" + + s3_url="s3://$S3_BUCKET/$S3_PREFIX/$role/$distro/$release/" + log_notice "Syncing to $s3_url" + $S3CMD sync ${S3_SYNC_ARGS[@]} "$upload_dir/" "$s3_url" + + # Create a timestamped directory to contain the old + # channel contents and move the old channel to it + mkdir -p "$archive_dir" + log_notice "Moving $release_dir to $archive_dir" + mv --no-target-directory "$release_dir" "$archive_dir" + + # Replace the old channel directory with the new one + log_notice "Updating $release_dir" + mv "$upload_dir" "$release_dir" + + rm -r "$tmp_dir" + else + log_notice "No new packages were staged in $staging_dir" + fi + done + done +done + +cleanup + +if [ "$NUM_ERRORS" -gt 0 ]; then + exit 5 +fi diff --git a/tests/data/packages/bar-1.0.0-0.tar.bz2 b/tests/data/packages/bar-1.0.0-0.tar.bz2 new file mode 100644 index 0000000000000000000000000000000000000000..ba61164f680111f5261c019d54bbf84031a46637 GIT binary patch literal 2286 zcmVZh{VyOMu0TaKmY&)ri4VrPbL!+ zB|k!XDd{~=B=rqFOn}kq00000;Aqi^G-;CvF#(9g(W6FyG}Ax;00fB&WHL0Tsp1Kz 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z?2X)@35L=QMZnmgvF1k!oXpxtwmn^naF(4~=af;`@!I)Adu-gZ;6l{1E>xkS#1=T2;Fqd-(kR6>CZrAwcnt$xxm(fa|9u)fJO94^ z{|o%JXjH@t?Z;vo(^owy?!AbaQdk>E7cRMS0%EPV1`v-B3#JzhD!30$!95e?ZASDw z2N3|hxa%-geKZVH@KT#5{ProgLFiXyWq~-;LqlJ&WtQw?)2n&2Zgg2ImZWoHE(nUh01V|uUNw(qvdDw&6nkOZz+nQniO1xI&4-qsgvpRPsHeYt! zYD@^_y45wU@CqvrT!0fGR49Ph1W<|J2P;c)3~;4F+PIMr6mY-=I-&?(Sb$jsGj_xU z2t1}|(@_#~9NUouX9mQ`)9HKT0p_V=T+&sO2uLuSAZg1asFXBnXA`X|nKQVSxN143 ztCL08WGKiznqK=uo`B_{>NX4@HJKe+Oam5=)xUF_!CGJvGcU>V-=E1ojvF3DmMwbE^L@sQz*( QLKprn "$PREFIX/bin/bar" < "$PREFIX/bin/baz" < "$PREFIX/bin/foo" < Date: Wed, 17 Oct 2018 09:54:30 +0100 Subject: [PATCH 002/119] Added monstrous freebayes build patch. Update to use new Conda compilers and split in bin/lib/dev subpackages. Use deb packages to build iRODS and remove Conda dependencies. Require build tools. --- recipes/bam_stats/1.13.0/Makefile.patch | 39 ++++++ recipes/bam_stats/1.13.0/build.sh | 8 +- recipes/bam_stats/1.13.0/meta.yaml | 16 ++- recipes/bambi/0.11.1/build.sh | 7 +- recipes/bambi/0.11.1/meta.yaml | 21 ++-- recipes/baton/1.1.0/build.sh | 11 +- recipes/baton/1.1.0/meta.yaml | 77 +++++++++--- recipes/bcftools/1.9/build.sh | 6 +- recipes/bcftools/1.9/meta.yaml | 15 ++- recipes/biobambam2/2.0.79/build.sh | 12 +- recipes/biobambam2/2.0.79/meta.yaml | 23 ++-- recipes/blat/35/build.sh | 7 +- recipes/blat/35/meta.yaml | 13 +- recipes/boost/1.68.0/build.sh | 31 +++++ recipes/boost/1.68.0/meta.yaml | 59 +++++++++ .../bowtie/1.0.0_dkj_fopen_with_mm/build.sh | 7 +- .../bowtie/1.0.0_dkj_fopen_with_mm/meta.yaml | 11 +- recipes/bowtie/1.2.2/build.sh | 7 +- recipes/bowtie/1.2.2/conda_build_config.yaml | 5 + recipes/bowtie/1.2.2/meta.yaml | 17 +-- recipes/bowtie2/2.2.7/build.sh | 4 +- recipes/bowtie2/2.2.7/meta.yaml | 13 +- recipes/bwa/0.7.17/build.sh | 6 +- recipes/bwa/0.7.17/meta.yaml | 15 +-- recipes/bzip2/1.0.6/Makefile-libbz2_so.patch | 25 ++++ recipes/bzip2/1.0.6/Makefile.patch | 48 +++++-- recipes/bzip2/1.0.6/build.sh | 13 +- recipes/bzip2/1.0.6/meta.yaml | 34 +++-- recipes/crumble/0.8/meta.yaml | 8 +- recipes/curl/7.58.0/build.sh | 7 +- recipes/curl/7.58.0/meta.yaml | 48 +++++-- recipes/eigen/3.3.4/build.sh | 6 +- recipes/eigen/3.3.4/meta.yaml | 5 +- recipes/fastx_toolkit/0.0.14/build.sh | 8 +- .../0.0.14/conda_build_config.yaml | 5 + recipes/fastx_toolkit/0.0.14/meta.yaml | 21 ++-- recipes/freebayes/1.2.0/Makefile.patch | 19 +++ .../freebayes/1.2.0/SeqLib_bwa_Makefile.patch | 32 +++++ .../1.2.0/SeqLib_fermi-lite_Makefile.patch | 17 +++ recipes/freebayes/1.2.0/build.sh | 13 +- recipes/freebayes/1.2.0/meta.yaml | 43 ++++--- recipes/freebayes/1.2.0/src/Makefile.patch | 20 --- recipes/freebayes/1.2.0/src_Makefile.patch | 76 +++++++++++ .../1.2.0/vcflib/tabixpp/Makefile.patch | 11 -- recipes/freebayes/1.2.0/vcflib_Makefile.patch | 11 ++ .../1.2.0/vcflib_tabixpp_Makefile.patch | 15 +++ .../vcflib_tabixpp_htslib_Makefile.patch | 42 +++++++ recipes/gmplib/6.1.2/build.sh | 6 +- recipes/gmplib/6.1.2/meta.yaml | 43 +++++-- recipes/gnutls/3.4.17/build.sh | 12 +- recipes/gnutls/3.4.17/meta.yaml | 82 +++++++++--- recipes/hdf5/1.10.1/build.sh | 10 +- recipes/hdf5/1.10.1/meta.yaml | 37 ++++-- recipes/hisat2/2.1.0/Makefile.patch | 13 ++ recipes/hisat2/2.1.0/build.sh | 9 +- recipes/hisat2/2.1.0/meta.yaml | 21 ++-- recipes/htslib/1.9+47-gc93b673/build.sh | 10 +- recipes/htslib/1.9+47-gc93b673/meta.yaml | 73 +++++++---- recipes/htslib/1.9+9-g6ec3b94/build.sh | 9 +- recipes/htslib/1.9+9-g6ec3b94/meta.yaml | 73 +++++++---- recipes/irods/4.1.12/build.sh | 21 +++- recipes/irods/4.1.12/conda_build_config.yaml | 6 + recipes/irods/4.1.12/meta.yaml | 34 +---- recipes/jansson/2.1.0/build.sh | 14 ++- recipes/jansson/2.1.0/meta.yaml | 40 ++++-- recipes/jq/1.5/build.sh | 4 +- recipes/jq/1.5/meta.yaml | 5 +- recipes/libgd/2.2.5/build.sh | 9 +- recipes/libgd/2.2.5/meta.yaml | 66 +++++++--- recipes/libmaus2/2.0.420/build.sh | 16 ++- recipes/libmaus2/2.0.420/meta.yaml | 65 ++++++---- recipes/libpng/1.6.34/build.sh | 12 ++ recipes/libpng/1.6.34/meta.yaml | 53 ++++++++ recipes/libpng/build.sh | 10 -- recipes/libpng/meta.yaml | 33 ----- recipes/libxml2/2.9.7/build.sh | 6 +- recipes/libxml2/2.9.7/meta.yaml | 66 +++++++--- recipes/libxslt/1.1.32/build.sh | 6 +- recipes/libxslt/1.1.32/meta.yaml | 71 ++++++++--- recipes/minimap2/2.10/build.sh | 6 +- recipes/minimap2/2.10/meta.yaml | 11 +- recipes/nanopolish/0.10.2/build.sh | 14 +++ recipes/nanopolish/0.10.2/meta.yaml | 35 ++++++ recipes/nettle/3.3/build.sh | 10 +- recipes/nettle/3.3/meta.yaml | 73 +++++++++-- recipes/npg_qc_utils/65.0/build.sh | 28 +++-- recipes/npg_qc_utils/65.0/meta.yaml | 25 ++-- recipes/openssl/1.0.2o/build.sh | 7 +- recipes/openssl/1.0.2o/meta.yaml | 58 +++++++-- recipes/pcre/8.41/build.sh | 9 +- recipes/pcre/8.41/meta.yaml | 74 ++++++++--- recipes/python-magic/0.4.15/meta.yaml | 5 +- recipes/rna-seqc/1.1.8/build.sh | 2 +- recipes/s3cmd/2.0.1-28-gd5e61c3/build.sh | 2 +- recipes/samtools/1.9+2-g02d93a1/build.sh | 10 +- recipes/samtools/1.9+2-g02d93a1/meta.yaml | 48 +++++-- recipes/staden_io_lib/1.14.10/build.sh | 10 -- recipes/staden_io_lib/1.14.10/meta.yaml | 119 ------------------ recipes/staden_io_lib/1.14.6/meta.yaml | 116 ++++++++++------- recipes/staden_io_lib/1.14.9/build.sh | 7 +- recipes/staden_io_lib/1.14.9/meta.yaml | 116 ++++++++++------- recipes/star/2.5.2b/build.sh | 4 +- recipes/star/2.5.2b/meta.yaml | 15 +-- recipes/tears/1.2.4/build.sh | 8 +- recipes/tears/1.2.4/meta.yaml | 20 +-- recipes/teepot/1.2.0/build.sh | 6 +- recipes/teepot/1.2.0/meta.yaml | 7 +- recipes/tophat2/2.1.1/build.sh | 10 +- recipes/tophat2/2.1.1/conda_build_config.yaml | 6 + recipes/tophat2/2.1.1/meta.yaml | 17 +-- recipes/verifybamid/1.1.3/build.sh | 15 +-- .../verifybamid/1.1.3/conda_build_config.yaml | 5 + recipes/verifybamid/1.1.3/libStatGen.patch | 73 +++++++++++ recipes/verifybamid/1.1.3/meta.yaml | 27 ++-- recipes/xz/5.2.3/build.sh | 6 +- recipes/xz/5.2.3/meta.yaml | 33 +++-- recipes/zlib/1.2.11/build.sh | 8 +- recipes/zlib/1.2.11/meta.yaml | 38 ++++-- 118 files changed, 2004 insertions(+), 971 deletions(-) create mode 100644 recipes/bam_stats/1.13.0/Makefile.patch mode change 100755 => 100644 recipes/bcftools/1.9/build.sh create mode 100644 recipes/boost/1.68.0/build.sh create mode 100644 recipes/boost/1.68.0/meta.yaml create mode 100644 recipes/bowtie/1.2.2/conda_build_config.yaml create mode 100644 recipes/bzip2/1.0.6/Makefile-libbz2_so.patch create mode 100644 recipes/fastx_toolkit/0.0.14/conda_build_config.yaml create mode 100644 recipes/freebayes/1.2.0/Makefile.patch create mode 100644 recipes/freebayes/1.2.0/SeqLib_bwa_Makefile.patch create mode 100644 recipes/freebayes/1.2.0/SeqLib_fermi-lite_Makefile.patch delete mode 100644 recipes/freebayes/1.2.0/src/Makefile.patch create mode 100644 recipes/freebayes/1.2.0/src_Makefile.patch delete mode 100644 recipes/freebayes/1.2.0/vcflib/tabixpp/Makefile.patch create mode 100644 recipes/freebayes/1.2.0/vcflib_Makefile.patch create mode 100644 recipes/freebayes/1.2.0/vcflib_tabixpp_Makefile.patch create mode 100644 recipes/freebayes/1.2.0/vcflib_tabixpp_htslib_Makefile.patch create mode 100644 recipes/hisat2/2.1.0/Makefile.patch create mode 100644 recipes/irods/4.1.12/conda_build_config.yaml create mode 100644 recipes/libpng/1.6.34/build.sh create mode 100644 recipes/libpng/1.6.34/meta.yaml delete mode 100644 recipes/libpng/build.sh delete mode 100644 recipes/libpng/meta.yaml create mode 100755 recipes/nanopolish/0.10.2/build.sh create mode 100644 recipes/nanopolish/0.10.2/meta.yaml delete mode 100755 recipes/staden_io_lib/1.14.10/build.sh delete mode 100644 recipes/staden_io_lib/1.14.10/meta.yaml create mode 100644 recipes/tophat2/2.1.1/conda_build_config.yaml create mode 100644 recipes/verifybamid/1.1.3/conda_build_config.yaml create mode 100644 recipes/verifybamid/1.1.3/libStatGen.patch diff --git a/recipes/bam_stats/1.13.0/Makefile.patch b/recipes/bam_stats/1.13.0/Makefile.patch new file mode 100644 index 00000000..e78e3fa2 --- /dev/null +++ b/recipes/bam_stats/1.13.0/Makefile.patch @@ -0,0 +1,39 @@ +diff --git c/Makefile c/Makefile +index 5b6474f..b2592d6 100644 +--- c/Makefile ++++ c/Makefile +@@ -2,14 +2,14 @@ + VERSION=$(shell perl -I../lib -MPCAP -e 'print PCAP->VERSION;') + + #Compiler +-CC = gcc -O3 -DVERSION='"$(VERSION)"' -g ++CC ?= gcc -O3 -DVERSION='"$(PKG_VERSION)"' -g + + #CC = gcc -O3 -DVERSION='"$(VERSION)"' -g + + #compiler flags + # -g adds debug info to the executable file + # -Wall turns on most warnings from compiler +-CFLAGS = -Wall ++CFLAGS ?= -Wall + + HTSLOC?=$(HTSLIB) + +@@ -64,7 +64,7 @@ all: clean make_htslib_tmp $(BAM_STATS_TARGET) test remove_htslib_tmp + @echo bam_stats compiled. + + $(BAM_STATS_TARGET): $(OBJS) +- $(CC) $(CFLAGS) $(INCLUDES) -o $(BAM_STATS_TARGET) $(OBJS) $(LFLAGS) $(LIBS) ./bam_stats.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(BAM_STATS_TARGET) $(OBJS) $(LFLAGS) $(LDFLAGS) $(LIBS) ./bam_stats.c + + #Unit Tests + test: $(BAM_STATS_TARGET) +@@ -98,7 +98,7 @@ valgrind: + # the rule(a .c file) and $@: the name of the target of the rule (a .o file) + # (see the gnu make manual section about automatic variables) + .c.o: +- $(CC) $(CFLAGS) $(INCLUDES) -c $< -o $@ ++ $(CC) $(CFLAGS) $(INCLUDES) $(CPPFLAGS) -c $< -o $@ + + clean: + @echo clean diff --git a/recipes/bam_stats/1.13.0/build.sh b/recipes/bam_stats/1.13.0/build.sh index 5dd802f3..38e25a8a 100755 --- a/recipes/bam_stats/1.13.0/build.sh +++ b/recipes/bam_stats/1.13.0/build.sh @@ -1,9 +1,11 @@ #!/bin/sh -set -e +set -ex cd ./c -perl -i -ple 's/^(\t\$\(CC\).*?)$/$1 \$(LDFLAGS) \$(LDLIBS)/smx' Makefile -make ../bin/bam_stats CFLAGS="-I./ -I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make ../bin/bam_stats CC="$GCC" \ + CFLAGS="-O3 -DVERSION='\"$PKG_VERSION\"' -g" \ + CPPFLAGS="-I$PREFIX/include" \ + LDFLAGS="-L$PREFIX/lib" cp ../bin/bam_stats "$PREFIX/bin/" diff --git a/recipes/bam_stats/1.13.0/meta.yaml b/recipes/bam_stats/1.13.0/meta.yaml index 72d2f2ee..ebddd8c5 100644 --- a/recipes/bam_stats/1.13.0/meta.yaml +++ b/recipes/bam_stats/1.13.0/meta.yaml @@ -10,23 +10,21 @@ about: summary: "Legacy, see cancerit/PCAP-core: NGS reference implementations and helper code for the IGCG/TCGA Pan-Cancer Analysis Project." build: - number: 0 + number: 1 source: git_url: https://github.com/ICGC-TCGA-PanCancer/PCAP-core.git git_rev: b8201e219ac7c7a7d968a23ea836b708a133deb8 - -features: - - irods + patches: + - Makefile.patch requirements: build: - - gcc_npg >=7.3 - - htslib >=1.7 - + - {{ compiler("c") }} + host: + - libhts-dev run: - - htslib >=1.7 - - zlib + - libhts test: commands: diff --git a/recipes/bambi/0.11.1/build.sh b/recipes/bambi/0.11.1/build.sh index 1a1c597a..c0e38156 100755 --- a/recipes/bambi/0.11.1/build.sh +++ b/recipes/bambi/0.11.1/build.sh @@ -1,12 +1,13 @@ #!/bin/sh -set -e +set -ex autoreconf -fi -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" -./configure --prefix="$PREFIX" --with-htslib="$PREFIX" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +./configure --prefix="$PREFIX" --with-htslib="$PREFIX" \ + CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install prefix="$PREFIX" diff --git a/recipes/bambi/0.11.1/meta.yaml b/recipes/bambi/0.11.1/meta.yaml index 88c229a8..065de0f6 100644 --- a/recipes/bambi/0.11.1/meta.yaml +++ b/recipes/bambi/0.11.1/meta.yaml @@ -10,7 +10,7 @@ about: summary: "A set of programs to manipulate SAM/BAM/CRAM files, using HTSLIB." build: - number: 2 + number: 3 source: git_url: https://github.com/wtsi-npg/bambi.git @@ -18,15 +18,22 @@ source: requirements: build: - - gcc_npg >=7.3 - - htslib >=1.9 - - libgd - - libxml2 - + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + - pkg-config + host: + - libgd-dev + - libhts-dev + - libxml2-dev + - libz-dev run: - - htslib >=1.9 - libgd + - libhts - libxml2 + - libz test: commands: diff --git a/recipes/baton/1.1.0/build.sh b/recipes/baton/1.1.0/build.sh index 593faefb..d48ce4b2 100755 --- a/recipes/baton/1.1.0/build.sh +++ b/recipes/baton/1.1.0/build.sh @@ -1,10 +1,13 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" -./configure --prefix="$PREFIX" --with-irods="$PREFIX" CPPFLAGS="-I$PREFIX/include/irods" LDFLAGS="-L$PREFIX/lib -L$PREFIX/lib/irods/externals" +./configure --prefix="$PREFIX" --with-irods="$PREFIX" \ + CPPFLAGS="-I$PREFIX/include/irods" \ + LDFLAGS="-L$PREFIX/lib -L$PREFIX/lib/irods/externals" -make -j $n +make -j $n CPPFLAGS="-I$PREFIX/include/irods" \ + LDFLAGS="-L$PREFIX/lib -L$PREFIX/lib/irods/externals" make install prefix="$PREFIX" diff --git a/recipes/baton/1.1.0/meta.yaml b/recipes/baton/1.1.0/meta.yaml index 67cc6e14..0a3df908 100644 --- a/recipes/baton/1.1.0/meta.yaml +++ b/recipes/baton/1.1.0/meta.yaml @@ -11,26 +11,73 @@ about: summary: Client programs and API for use with iRODS (Integrated Rule-Oriented Data System). build: - number: 1 + number: 2 source: url: https://github.com/wtsi-npg/baton/releases/download/{{ version }}/baton-{{ version }}.tar.gz fn: baton-{{ version }}.tar.gz sha256: {{ sha256 }} -features: - - irods +outputs: + - name: baton + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - libtool + - make + - perl + - pkg-config + host: + - irods-dev ==4.1.12 + - libjansson-dev + - libssl-dev + run: + - {{ pin_subpackage("libbaton", exact=True) }} + - irods-plugins ==4.1.12 + - libjansson + - libssl + files: + - bin/baton-* + test: + commands: + - baton-list --version -requirements: - build: - - gcc_npg - - irods-dev ==4.1.12 - - jansson + - name: libbaton + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - libtool + - make + - perl + - pkg-config + host: + - irods-dev ==4.1.12 + - libjansson-dev + - libssl-dev + run: + - irods-plugins ==4.1.12 + - libjansson + - libssl + files: + - lib/libbaton.* + test: + commands: + - test -h ${PREFIX}/lib/libbaton.so - run: - - irods-plugins ==4.1.12 - - jansson - -test: - commands: - - baton-list --version + - name: libbaton-dev + version: {{ version }} + requirements: + run: + {{ pin_subpackage("libbaton", exact=True) }} + files: + - include/baton + - lib/pkgconfig/baton.pc + test: + commands: + - test -f ${PREFIX}/include/baton/baton.h diff --git a/recipes/bcftools/1.9/build.sh b/recipes/bcftools/1.9/build.sh old mode 100755 new mode 100644 index caf5544c..25565d17 --- a/recipes/bcftools/1.9/build.sh +++ b/recipes/bcftools/1.9/build.sh @@ -1,10 +1,10 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" ./configure --prefix="$PREFIX" --with-htslib="$PREFIX" -make -j $n +make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install prefix="$PREFIX" diff --git a/recipes/bcftools/1.9/meta.yaml b/recipes/bcftools/1.9/meta.yaml index 3ff31b57..0fa0d7e1 100644 --- a/recipes/bcftools/1.9/meta.yaml +++ b/recipes/bcftools/1.9/meta.yaml @@ -12,8 +12,8 @@ about: summary: VCF commands and BCF calling. build: - number: 0 - + number: 1 + source: url: https://github.com/samtools/bcftools/releases/download/{{ version }}/bcftools-{{ version }}.tar.bz2 fn: bcftools-{{ version }}.tar.bz2 @@ -21,11 +21,14 @@ source: requirements: build: - - gcc_npg >=7.3 - - htslib >={{ version }},<{{ maxversion }} - + - {{ compiler("c") }} + - make + host: + - libhts-dev >={{ version }},<{{ maxversion }} + - libz-dev run: - - htslib >={{ version }},<{{ maxversion }} + - libhts >={{ version }},<{{ maxversion }} + - libz test: commands: diff --git a/recipes/biobambam2/2.0.79/build.sh b/recipes/biobambam2/2.0.79/build.sh index 168118e6..beae12d6 100755 --- a/recipes/biobambam2/2.0.79/build.sh +++ b/recipes/biobambam2/2.0.79/build.sh @@ -1,10 +1,14 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" -./configure --prefix="$PREFIX" --with-libmaus2="$PREFIX" LDFLAGS="-L$PREFIX/lib -L$PREFIX/lib/irods/externals" LIBS="-lirods_client_api -lrt" +./configure --prefix="$PREFIX" \ + --with-libmaus2="$PREFIX" \ + LDFLAGS="-L$PREFIX/lib -L$PREFIX/lib/irods/externals" \ + LIBS="-lirods_client_api -lrt" -make -j $n +make -j $n CPPFLAGS="-I$PREFIX/include" \ + LDFLAGS="-L$PREFIX/lib -L$PREFIX/lib/irods/externals" make install prefix="$PREFIX" diff --git a/recipes/biobambam2/2.0.79/meta.yaml b/recipes/biobambam2/2.0.79/meta.yaml index e98a5740..9fb980a9 100644 --- a/recipes/biobambam2/2.0.79/meta.yaml +++ b/recipes/biobambam2/2.0.79/meta.yaml @@ -11,11 +11,7 @@ about: summary: Tools for early stage alignment file processing. build: - number: 0 - - rpaths: - - lib64 - - lib + number: 1 source: url: https://github.com/gt1/biobambam2/archive/{{ version }}-release-20171006114010.tar.gz @@ -24,15 +20,20 @@ source: requirements: build: - - gcc_npg >=7.3 + - {{ compiler("cxx") }} + - make + - pkg-config + host: - irods-dev - - libmaus2 - - zlib - + - libgnutls-dev + - libmaus2-dev + - libnettle-dev + - libz-dev run: - - libgcc_npg >=7.3 + - libgnutls - libmaus2 - - zlib + - libnettle + - libz test: commands: diff --git a/recipes/blat/35/build.sh b/recipes/blat/35/build.sh index fd9a2931..8e0eef53 100755 --- a/recipes/blat/35/build.sh +++ b/recipes/blat/35/build.sh @@ -1,11 +1,12 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" mkdir -p "$SRC_DIR/bin" -make -j $n MACHTYPE=X86_64 BINDIR="$SRC_DIR/bin" +make -j $n MACHTYPE=X86_64 BINDIR="$SRC_DIR/bin" \ + CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" mkdir -p "$PREFIX/bin" diff --git a/recipes/blat/35/meta.yaml b/recipes/blat/35/meta.yaml index ba3120f3..343740b8 100644 --- a/recipes/blat/35/meta.yaml +++ b/recipes/blat/35/meta.yaml @@ -7,11 +7,11 @@ package: about: home: http://genome.ucsc.edu/ - license: Blat + license: Other summary: "Rapid mRNA/DNA and cross-species protein alignments." build: - number: 1 + number: 2 source: url: https://users.soe.ucsc.edu/~kent/src/blatSrc{{ version }}.zip @@ -20,11 +20,14 @@ source: requirements: build: - - gcc_npg >=7.3 - - libpng - + - {{ compiler("c") }} + - make + host: + - libpng-dev + - libz-dev run: - libpng + - libz test: commands: diff --git a/recipes/boost/1.68.0/build.sh b/recipes/boost/1.68.0/build.sh new file mode 100644 index 00000000..181044d6 --- /dev/null +++ b/recipes/boost/1.68.0/build.sh @@ -0,0 +1,31 @@ +#!/bin/sh + +set -ex + +n="$CPU_COUNT" + +# bootstrap fails because it has the gcc target name hard-coded as +# 'gcc' and doesn't respect Conda's "$GCC" environment variable: + +shopt -u | grep -q nullglob && nullglob_enabled=0 +[ $nullglob_enabled ] || shopt -s nullglob + +for f in ar as c++ cc cpp g++ gcc gcc-ar gcc-nm gcc-ranlib ld; do + fullname=($BUILD_PREFIX/bin/*-$f) + shortname="$BUILD_PREFIX/bin/$f" + [ -h "$shortname" ] || ln -s "$fullname" "$shortname" +done + +[ $nullglob_enabled ] || shopt -u nullglob + +./bootstrap.sh --prefix="$PREFIX" --with-toolset=gcc + +# The cxxflags and linkflags options are not well documented. They do +# not appear in `./b2 --help` and are only mentioned in the HTML docs +# for the "sun" toolset. +./b2 -j $n --prefix="$PREFIX" --layout=system \ + cxxflags="-I$PREFIX/include" \ + linkflags="-L$PREFIX/lib" \ + link=shared runtime-link=shared \ + threading=multi variant=release \ + install diff --git a/recipes/boost/1.68.0/meta.yaml b/recipes/boost/1.68.0/meta.yaml new file mode 100644 index 00000000..91fc082f --- /dev/null +++ b/recipes/boost/1.68.0/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.68.0" %} +{% set alt_version = "1_68_0" %} +{% set sha256 = "7f6130bc3cf65f56a618888ce9d5ea704fa10b462be126ad053e80e553d6d8b7" %} + +package: + name: boost + version: "{{ version }}" + +about: + home: http://www.boost.org + license: Other + summary: "Free peer-reviewed portable C++ source libraries." + +build: + number: 0 + +source: + url: https://dl.bintray.com/boostorg/release/{{ version }}/source/boost_{{ alt_version }}.tar.bz2 + fn: boost_{{ alt_version }}.tar.bz2 + sha256: {{ sha256 }} + +requirements: + build: + - {{ compiler("cxx") }} + run: + - {{ pin_subpackage("libboost-dev", exact=True) }} + +outputs: + - name: libboost + version: {{ version }} + requirements: + build: + - {{ compiler("cxx") }} + - make + host: + - libbz2-dev + - liblzma-dev + - libz-dev + run: + - libbz2 + - liblzma + - libz + files: + - lib/libboost* + test: + commands: + - test -f ${PREFIX}/lib/libboost_system.a + - test -h ${PREFIX}/lib/libboost_system.so + + - name: libboost-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libboost", exact=True) }} + files: + - include/boost + test: + commands: + - test -f ${PREFIX}/include/boost/config.hpp diff --git a/recipes/bowtie/1.0.0_dkj_fopen_with_mm/build.sh b/recipes/bowtie/1.0.0_dkj_fopen_with_mm/build.sh index 8ad20373..037efa95 100755 --- a/recipes/bowtie/1.0.0_dkj_fopen_with_mm/build.sh +++ b/recipes/bowtie/1.0.0_dkj_fopen_with_mm/build.sh @@ -1,10 +1,11 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" -make -j $n prefix="$PREFIX" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make -j $n prefix="$PREFIX" CC="$GCC" CPP="$CXX" \ + CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" # There is no install target in the Makefile mkdir -p "$PREFIX/bin" diff --git a/recipes/bowtie/1.0.0_dkj_fopen_with_mm/meta.yaml b/recipes/bowtie/1.0.0_dkj_fopen_with_mm/meta.yaml index e4de06c8..18c53f7f 100644 --- a/recipes/bowtie/1.0.0_dkj_fopen_with_mm/meta.yaml +++ b/recipes/bowtie/1.0.0_dkj_fopen_with_mm/meta.yaml @@ -10,11 +10,7 @@ about: summary: An ultrafast memory-efficient short read aligner. build: - number: 0 - - rpaths: - - lib64 - - lib + number: 1 source: git_url: https://github.com/dkj/bowtie.git @@ -22,10 +18,7 @@ source: requirements: build: - - gcc_npg >=7.3 - - run: - - libgcc_npg >=7.3 + - {{ compiler("cxx") }} test: commands: diff --git a/recipes/bowtie/1.2.2/build.sh b/recipes/bowtie/1.2.2/build.sh index 8ad20373..1d650cb3 100755 --- a/recipes/bowtie/1.2.2/build.sh +++ b/recipes/bowtie/1.2.2/build.sh @@ -1,10 +1,11 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" -make -j $n prefix="$PREFIX" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make -j $n prefix="$PREFIX" CC="$GCC" CPP="$CXX" \ + EXTRA_CXXFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" # There is no install target in the Makefile mkdir -p "$PREFIX/bin" diff --git a/recipes/bowtie/1.2.2/conda_build_config.yaml b/recipes/bowtie/1.2.2/conda_build_config.yaml new file mode 100644 index 00000000..54d7f516 --- /dev/null +++ b/recipes/bowtie/1.2.2/conda_build_config.yaml @@ -0,0 +1,5 @@ +c_compiler_version: + - 5.4 + +cxx_compiler_version: + - 5.4 diff --git a/recipes/bowtie/1.2.2/meta.yaml b/recipes/bowtie/1.2.2/meta.yaml index 5821a816..f7b54ab8 100644 --- a/recipes/bowtie/1.2.2/meta.yaml +++ b/recipes/bowtie/1.2.2/meta.yaml @@ -10,11 +10,7 @@ about: summary: An ultrafast memory-efficient short read aligner. build: - number: 1 - - rpaths: - - lib64 - - lib + number: 2 source: git_url: https://github.com/BenLangmead/bowtie @@ -22,14 +18,13 @@ source: requirements: build: - - gcc_npg <7.3 - - tbb - - zlib - + - gcc # Needs g++ 4.8 + host: + - tbb-devel + - libz-dev run: - - libgcc_npg <7.3 - tbb - - zlib + - libz test: commands: diff --git a/recipes/bowtie2/2.2.7/build.sh b/recipes/bowtie2/2.2.7/build.sh index c6350e51..2ad5ef89 100755 --- a/recipes/bowtie2/2.2.7/build.sh +++ b/recipes/bowtie2/2.2.7/build.sh @@ -1,8 +1,8 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" make -j $n prefix="$PREFIX" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" diff --git a/recipes/bowtie2/2.2.7/meta.yaml b/recipes/bowtie2/2.2.7/meta.yaml index a4b03a4a..f5402406 100644 --- a/recipes/bowtie2/2.2.7/meta.yaml +++ b/recipes/bowtie2/2.2.7/meta.yaml @@ -6,15 +6,11 @@ package: about: home: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml - license: GPLv3 + license: GPL3 summary: "A fast and sensitive gapped read aligner." build: - number: 1 - - rpaths: - - lib64 - - lib + number: 2 source: git_url: https://github.com/BenLangmead/bowtie2.git @@ -22,10 +18,7 @@ source: requirements: build: - - gcc_npg >=5.5,<7.0.0 - - run: - - libgcc_npg >=5.5 + - {{ compiler("cxx") }} test: commands: diff --git a/recipes/bwa/0.7.17/build.sh b/recipes/bwa/0.7.17/build.sh index 1df2b5d9..5b0ed0e8 100755 --- a/recipes/bwa/0.7.17/build.sh +++ b/recipes/bwa/0.7.17/build.sh @@ -1,10 +1,10 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" -make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make -j $n CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" mkdir -p "$PREFIX/bin" cp bwa "$PREFIX/bin/" diff --git a/recipes/bwa/0.7.17/meta.yaml b/recipes/bwa/0.7.17/meta.yaml index 46c1be5f..e48ceb3c 100644 --- a/recipes/bwa/0.7.17/meta.yaml +++ b/recipes/bwa/0.7.17/meta.yaml @@ -1,30 +1,31 @@ {% set version = "0.7.17" %} package: - name: bwa-aligner + name: bwa version: "{{ version }}" about: home: https://github.com/lh3/bwa - license: GPLv3 + license: GPL3 summary: Burrows-Wheeler Aligner for short-read alignment. build: - number: 1 + number: 2 source: - git_url: https://github.com/lh3/bwa.git git_rev: v{{ version }} - patches: - Makefile.patch requirements: build: - - zlib - + - {{ compiler("c") }} + - make + host: + - libz-dev run: - - zlib + - libz test: commands: diff --git a/recipes/bzip2/1.0.6/Makefile-libbz2_so.patch b/recipes/bzip2/1.0.6/Makefile-libbz2_so.patch new file mode 100644 index 00000000..983b7994 --- /dev/null +++ b/recipes/bzip2/1.0.6/Makefile-libbz2_so.patch @@ -0,0 +1,25 @@ +*** Makefile-libbz2_so 2010-09-11 00:07:52.000000000 +0100 +--- Makefile-libbz2_so.patch 2018-09-05 14:36:07.365334104 +0100 +*************** +*** 22,30 **** + + + SHELL=/bin/sh +! CC=gcc + BIGFILES=-D_FILE_OFFSET_BITS=64 +! CFLAGS=-fpic -fPIC -Wall -Winline -O2 -g $(BIGFILES) + + OBJS= blocksort.o \ + huffman.o \ +--- 22,32 ---- + + + SHELL=/bin/sh +! CC?=gcc + BIGFILES=-D_FILE_OFFSET_BITS=64 +! CFLAGS?=-fpic -fPIC -Wall -Winline -O2 -g $(BIGFILES) +! +! PREFIX="$PREFIX" + + OBJS= blocksort.o \ + huffman.o \ diff --git a/recipes/bzip2/1.0.6/Makefile.patch b/recipes/bzip2/1.0.6/Makefile.patch index 9e3d0b13..98872f60 100644 --- a/recipes/bzip2/1.0.6/Makefile.patch +++ b/recipes/bzip2/1.0.6/Makefile.patch @@ -1,11 +1,37 @@ ---- Makefile 2010-09-10 23:46:02.000000000 +0100 -+++ Makefile.fpic 2018-02-01 18:49:09.204566000 +0000 -@@ -21,7 +21,7 @@ - LDFLAGS= - - BIGFILES=-D_FILE_OFFSET_BITS=64 --CFLAGS=-Wall -Winline -O2 -g $(BIGFILES) -+CFLAGS=-Wall -Winline -O2 -g $(BIGFILES) -fPIC - - # Where you want it installed when you do 'make install' - PREFIX=/usr/local +*** Makefile 2010-09-10 23:46:02.000000000 +0100 +--- Makefile.patch 2018-09-05 14:36:38.896339103 +0100 +*************** +*** 15,31 **** + SHELL=/bin/sh + + # To assist in cross-compiling +! CC=gcc +! AR=ar +! RANLIB=ranlib +! LDFLAGS= + + BIGFILES=-D_FILE_OFFSET_BITS=64 +! CFLAGS=-Wall -Winline -O2 -g $(BIGFILES) + + # Where you want it installed when you do 'make install' +! PREFIX=/usr/local +! + + OBJS= blocksort.o \ + huffman.o \ +--- 15,29 ---- + SHELL=/bin/sh + + # To assist in cross-compiling +! CC?=gcc +! AR?=ar +! RANLIB?=ranlib + + BIGFILES=-D_FILE_OFFSET_BITS=64 +! CFLAGS?=-Wall -Winline -O2 -g $(BIGFILES) + + # Where you want it installed when you do 'make install' +! PREFIX="$PREFIX" + + OBJS= blocksort.o \ + huffman.o \ diff --git a/recipes/bzip2/1.0.6/build.sh b/recipes/bzip2/1.0.6/build.sh index 8f68fa50..33212715 100644 --- a/recipes/bzip2/1.0.6/build.sh +++ b/recipes/bzip2/1.0.6/build.sh @@ -1,9 +1,14 @@ #!/bin/sh -set -e +set -ex +n="$CPU_COUNT" + +CFLAGS="$CFLAGS -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -fPIC" + +make -j $n CC="$GCC" PREFIX="$PREFIX" CFLAGS="$CFLAGS" make PREFIX="$PREFIX" install -make clean +make -f Makefile-libbz2_so CC="$GCC" PREFIX="$PREFIX" CFLAGS="$CFLAGS" -make -f Makefile-libbz2_so PREFIX="$PREFIX" -cp -a libbz2.so* "$PREFIX/lib" +cp -a libbz2.so* "$PREFIX/lib/" +ln -s "$PREFIX/lib/libbz2.so.1.0" "$PREFIX/lib/libbz2.so" diff --git a/recipes/bzip2/1.0.6/meta.yaml b/recipes/bzip2/1.0.6/meta.yaml index 138b9e97..e62abaed 100644 --- a/recipes/bzip2/1.0.6/meta.yaml +++ b/recipes/bzip2/1.0.6/meta.yaml @@ -11,25 +11,25 @@ about: summary: Data compressor. build: - number: 2 - + number: 3 + source: url: http://http.debian.net/debian/pool/main/b/bzip2/bzip2_{{ version }}.orig.tar.bz2 fn: bzip2-{{ version }}.tar.gz sha256: {{ sha256 }} patches: - Makefile.patch - -requirements: - build: - - gcc_npg >=7.3.0 + - Makefile-libbz2_so.patch outputs: - name: bzip2 version: {{ version }} requirements: + build: + - {{ compiler("c") }} + - make run: - - libbzip2 =={{ version }} + - {{ pin_subpackage('libbz2', exact=True) }} files: - bin/bunzip2 - bin/bzcat @@ -48,13 +48,25 @@ outputs: - bzip2 --help - bunzip2 --help - - name: libbzip2 + - name: libbz2 version: {{ version }} + requirements: + build: + - {{ compiler("c") }} files: - - include - - lib + - lib/libbz2.* test: commands: - - test -f ${PREFIX}/include/bzlib.h - test -f ${PREFIX}/lib/libbz2.a - test -h ${PREFIX}/lib/libbz2.so.1.0 + + - name: libbz2-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage('libbz2', exact=True) }} + files: + - include + test: + commands: + - test -f ${PREFIX}/include/bzlib.h diff --git a/recipes/crumble/0.8/meta.yaml b/recipes/crumble/0.8/meta.yaml index ae6fa5eb..41ea3685 100644 --- a/recipes/crumble/0.8/meta.yaml +++ b/recipes/crumble/0.8/meta.yaml @@ -19,11 +19,11 @@ source: requirements: build: - - gcc_npg >=7.3 - - htslib >=1.7 - + - {{ compiler("c") }} + host: + - libhts-dev run: - - htslib >=1.7 + - libhts test: commands: diff --git a/recipes/curl/7.58.0/build.sh b/recipes/curl/7.58.0/build.sh index 2b9f2857..25fa9870 100755 --- a/recipes/curl/7.58.0/build.sh +++ b/recipes/curl/7.58.0/build.sh @@ -1,13 +1,14 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" ./configure prefix="$PREFIX" \ --with-gnutls="$PREFIX" \ --with-zlib="$PREFIX" \ --without-ssl \ CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make -j $n + +make -j $n LDFLAGS="-Wl,-rpath-link,$PREFIX/lib -Wl,--disable-new-dtags -L$PREFIX/lib" make install prefix="$PREFIX" diff --git a/recipes/curl/7.58.0/meta.yaml b/recipes/curl/7.58.0/meta.yaml index 34aaf3ae..cf753869 100644 --- a/recipes/curl/7.58.0/meta.yaml +++ b/recipes/curl/7.58.0/meta.yaml @@ -11,24 +11,28 @@ about: summary: Command line tool and library for transferring data with URLs. build: - number: 1 + number: 2 source: - url: http://curl.haxx.se/download/curl-{{ version }}.tar.bz2 sha256: {{ sha256 }} -requirements: - build: - - gcc_npg >=7.3 - - gnutls - - zlib - outputs: - name: curl version: {{ version }} requirements: + build: + - {{ compiler("c") }} + - make + host: + - libgnutls-dev + - libnettle-dev + - libz-dev run: - - libcurl =={{ version}} + - {{ pin_subpackage("libcurl", exact=True) }} + - libgnutls + - libnettle + - libz files: - bin/curl - bin/curl-config @@ -39,18 +43,36 @@ outputs: - curl -h - name: libcurl + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - make + host: + - libgnutls-dev + - libnettle-dev + - libz-dev + run: + - libgnutls + - libnettle + - libz + files: + - lib/libcurl.a + - lib/libcurl.so* + test: + commands: + - test -f ${PREFIX}/lib/libcurl.a + - test -h ${PREFIX}/lib/libcurl.so + + - name: libcurl-dev version: {{ version }} requirements: run: - - gnutls - - zlib + - {{ pin_subpackage("libcurl", exact=True) }} files: - include/curl - - lib/libcurl* - lib/pkgconfig/libcurl.pc - share/man/man4/libcurl* test: commands: - test -f ${PREFIX}/include/curl/curl.h - - test -f ${PREFIX}/lib/libcurl.a - - test -h ${PREFIX}/lib/libcurl.so diff --git a/recipes/eigen/3.3.4/build.sh b/recipes/eigen/3.3.4/build.sh index 52c843b9..4c07125c 100755 --- a/recipes/eigen/3.3.4/build.sh +++ b/recipes/eigen/3.3.4/build.sh @@ -1,11 +1,11 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" mkdir build cd build cmake -DCMAKE_INSTALL_PREFIX="$PREFIX" .. -make -j $n install +make -j $n install CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" diff --git a/recipes/eigen/3.3.4/meta.yaml b/recipes/eigen/3.3.4/meta.yaml index b38278ca..c54cbf7b 100644 --- a/recipes/eigen/3.3.4/meta.yaml +++ b/recipes/eigen/3.3.4/meta.yaml @@ -11,7 +11,7 @@ about: summary: "A C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms." build: - number: 0 + number: 1 source: url: https://bitbucket.org/eigen/eigen/get/{{ version }}.tar.bz2 @@ -19,5 +19,6 @@ source: requirements: build: + - {{ compiler("cxx") }} - cmake - - gcc_npg >=7.3 + diff --git a/recipes/fastx_toolkit/0.0.14/build.sh b/recipes/fastx_toolkit/0.0.14/build.sh index c0d0d15c..3ba14a7c 100755 --- a/recipes/fastx_toolkit/0.0.14/build.sh +++ b/recipes/fastx_toolkit/0.0.14/build.sh @@ -1,17 +1,17 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" pushd gtextutils ./configure --prefix="$PREFIX" -make -j $n +make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install prefix="$PREFIX" popd pushd fastx_toolkit ./configure --prefix="$PREFIX" -make -j $n +make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install prefix="$PREFIX" popd diff --git a/recipes/fastx_toolkit/0.0.14/conda_build_config.yaml b/recipes/fastx_toolkit/0.0.14/conda_build_config.yaml new file mode 100644 index 00000000..54d7f516 --- /dev/null +++ b/recipes/fastx_toolkit/0.0.14/conda_build_config.yaml @@ -0,0 +1,5 @@ +c_compiler_version: + - 5.4 + +cxx_compiler_version: + - 5.4 diff --git a/recipes/fastx_toolkit/0.0.14/meta.yaml b/recipes/fastx_toolkit/0.0.14/meta.yaml index 72b8bf99..2ddba559 100644 --- a/recipes/fastx_toolkit/0.0.14/meta.yaml +++ b/recipes/fastx_toolkit/0.0.14/meta.yaml @@ -13,11 +13,7 @@ about: summary: "A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing." build: - number: 0 - - rpaths: - - lib64 - - lib + number: 1 source: - url: https://github.com/agordon/fastx_toolkit/releases/download/{{ version }}/fastx_toolkit-{{ version }}.tar.bz2 @@ -28,13 +24,16 @@ source: folder: gtextutils sha256: {{ gtextutils_sha256 }} -requirements: - build: - - gcc_npg <7.3 +outputs: + - name: fastx_toolkit + version: {{ version }} + requirements: + build: + - {{ compiler("cxx") }} + - make + files: + - bin/fast* - run: - - libgcc_npg <7.3 - test: commands: - test -x ${PREFIX}/bin/fastx_clipper diff --git a/recipes/freebayes/1.2.0/Makefile.patch b/recipes/freebayes/1.2.0/Makefile.patch new file mode 100644 index 00000000..533246e6 --- /dev/null +++ b/recipes/freebayes/1.2.0/Makefile.patch @@ -0,0 +1,19 @@ +--- Makefile 2018-10-12 08:09:44.857349600 +0100 ++++ Makefile.1 2018-10-12 08:08:12.901626040 +0100 +@@ -1,11 +1,12 @@ +-all: vcflib/Makefile log ++all: vcflib/Makefile # log + cd src && $(MAKE) + +-wbamtools: vcflib/Makefile log ++wbamtools: vcflib/Makefile # log + cd src && $(MAKE) -f Makefile.bamtools + +-log: src/version_git.h +- wget -q http://hypervolu.me/freebayes/build/$(shell cat src/version_git.h | grep v | cut -f 3 -d\ | sed s/\"//g) & ++# Oh, no you don't ... ++# log: src/version_git.h ++# wget -q http://hypervolu.me/freebayes/build/$(shell cat src/version_git.h | grep v | cut -f 3 -d\ | sed s/\"//g) & + + src/version_git.h: + cd src && $(MAKE) autoversion diff --git a/recipes/freebayes/1.2.0/SeqLib_bwa_Makefile.patch b/recipes/freebayes/1.2.0/SeqLib_bwa_Makefile.patch new file mode 100644 index 00000000..5a31ea76 --- /dev/null +++ b/recipes/freebayes/1.2.0/SeqLib_bwa_Makefile.patch @@ -0,0 +1,32 @@ +--- SeqLib/bwa/Makefile 2018-10-12 08:14:57.025171401 +0100 ++++ SeqLib/bwa/Makefile.1 2018-10-12 08:13:08.752688957 +0100 +@@ -1,8 +1,8 @@ +-CC= gcc ++CC?= gcc + #CC= clang --analyze + CFLAGS= -g -Wall -Wno-unused-function -O2 + WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS +-AR= ar ++AR?= ar + DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) + ## moved is.o bwtiindex.o rope.o to LOBJS + LOBJS= utils.o kthread.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o \ +@@ -23,15 +23,15 @@ + .SUFFIXES:.c .o .cc + + .c.o: +- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ ++ $(CC) -c $(CFLAGS) $(DFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@ + + all:$(PROG) + + bwa:libbwa.a $(AOBJS) main.o +- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) ++ $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. $(LDFLAGS) -lbwa $(LIBS) + + bwamem-lite:libbwa.a example.o +- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) ++ $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. $(LDFLAGS) -lbwa $(LIBS) + + libbwa.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) diff --git a/recipes/freebayes/1.2.0/SeqLib_fermi-lite_Makefile.patch b/recipes/freebayes/1.2.0/SeqLib_fermi-lite_Makefile.patch new file mode 100644 index 00000000..387c7dfa --- /dev/null +++ b/recipes/freebayes/1.2.0/SeqLib_fermi-lite_Makefile.patch @@ -0,0 +1,17 @@ +--- SeqLib/fermi-lite/Makefile 2018-10-12 08:21:20.404073207 +0100 ++++ SeqLib/fermi-lite/Makefile.1 2018-10-12 08:21:05.621086268 +0100 +@@ -1,4 +1,4 @@ +-CC= gcc ++CC?= gcc + CFLAGS= -g -Wall -O2 -Wno-unused-function #-fno-inline-functions -fno-inline-functions-called-once + CPPFLAGS= + INCLUDES= +@@ -17,7 +17,7 @@ + all:$(PROG) + + fml-asm:libfml.a example.o +- $(CC) $(CFLAGS) $^ -o $@ -L. -lfml $(LIBS) ++ $(CC) $(CFLAGS) $^ -o $@ -L. -lfml $(LDFLAGS) $(LIBS) + + libfml.a:$(OBJS) + $(AR) -csru $@ $(OBJS) diff --git a/recipes/freebayes/1.2.0/build.sh b/recipes/freebayes/1.2.0/build.sh index 8c4be7bf..4bc047ac 100755 --- a/recipes/freebayes/1.2.0/build.sh +++ b/recipes/freebayes/1.2.0/build.sh @@ -1,12 +1,11 @@ #!/bin/sh -set -e +set -ex -export CXXFLAGS="-I$PREFIX/include" -export LDFLAGS="-L$PREFIX/lib" -export CPPFLAGS="-I$PREFIX/include" - -make -j 1 +make -j 1 CC="$GCC" CXX="$CXX" \ + CXXFLAGS="-I$PREFIX/include" \ + CPPFLAGS="-I$PREFIX/include" \ + LDFLAGS="-L$PREFIX/lib" mkdir -p "$PREFIX/bin" -cp bin/freebayes bin/bamleftalign $PREFIX/bin/ +cp bin/freebayes bin/bamleftalign "$PREFIX/bin/" diff --git a/recipes/freebayes/1.2.0/meta.yaml b/recipes/freebayes/1.2.0/meta.yaml index 715cd531..4d1be319 100644 --- a/recipes/freebayes/1.2.0/meta.yaml +++ b/recipes/freebayes/1.2.0/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "v1.2.0" %} +{% set version = "1.2.0" %} package: name: freebayes @@ -10,34 +10,39 @@ about: summary: Bayesian haplotype-based genetic polymorphism discovery and genotyping. build: - number: 0 - rpaths: - - lib64 - - lib + number: 1 source: git_url: https://github.com/ekg/freebayes.git - git_tag: {{ version }} + git_tag: v{{ version }} patches: - - src/Makefile.patch - - vcflib/tabixpp/Makefile.patch + - Makefile.patch + - src_Makefile.patch + - SeqLib_bwa_Makefile.patch + - SeqLib_fermi-lite_Makefile.patch + - vcflib_Makefile.patch + - vcflib_tabixpp_Makefile.patch + - vcflib_tabixpp_htslib_Makefile.patch requirements: build: - - libbzip2 - - libcurl - - gcc_npg >=7.3 - - liblzma - - openssl - - zlib - + - {{ compiler("c") }} + - {{ compiler("cxx") }} + - automake + - make + - perl + host: + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libssl-dev + - libz-dev run: - - libbzip2 + - libbz2 - libcurl - - libgcc_npg >=7.3 - liblzma - - openssl - - zlib + - libssl + - libz test: commands: diff --git a/recipes/freebayes/1.2.0/src/Makefile.patch b/recipes/freebayes/1.2.0/src/Makefile.patch deleted file mode 100644 index e69f60ae..00000000 --- a/recipes/freebayes/1.2.0/src/Makefile.patch +++ /dev/null @@ -1,20 +0,0 @@ ---- src/Makefile 2018-09-07 14:27:44.368935165 +0000 -+++ src/Makefile.lib 2018-09-07 14:27:32.380857346 +0000 -@@ -46,7 +46,7 @@ - .PHONY: all static debug profiling gprof - - $(HTSLIB_ROOT)/libhts.a: -- cd $(HTSLIB_ROOT) && make -+ cd $(HTSLIB_ROOT) && make LDFLAGS="-L$(PREFIX)/lib" CPPFLAGS="-I$(PREFIX)/include" - - $(SEQLIB_ROOT)/src/libseqlib.a: - cd $(SEQLIB_ROOT) && ./configure && make -@@ -256,7 +256,7 @@ - autoversion: - @( \ - if [ -d "../.git" ] && which git > /dev/null ; then \ -- DETECTED_VERSION=$$(git describe --always --tags --dirty) ; \ -+ DETECTED_VERSION=$$(git describe --always --tags) ; \ - else \ - DETECTED_VERSION=$$(grep -v "^#" "$(RELEASED_VERSION_FILE)") ; \ - fi ; \ diff --git a/recipes/freebayes/1.2.0/src_Makefile.patch b/recipes/freebayes/1.2.0/src_Makefile.patch new file mode 100644 index 00000000..92d10d39 --- /dev/null +++ b/recipes/freebayes/1.2.0/src_Makefile.patch @@ -0,0 +1,76 @@ +--- src/Makefile 2018-10-12 08:11:34.258250893 +0100 ++++ src/Makefile.1 2018-10-12 08:11:18.992508942 +0100 +@@ -5,11 +5,10 @@ + ################################################################################ + + # Compiler +-CXX=g++ ${CXXFLAGS} +-C=gcc ++CXX?=g++ ${CXXFLAGS} ++CC?=gcc + + export CXXFLAGS +-export C + export CC + export CXX + export LDFLAGS +@@ -26,7 +25,7 @@ + HTSLIB_ROOT=$(SEQLIB_ROOT)/htslib + + LIBS = -lz -llzma -lbz2 -lm -lpthread +-INCLUDE = -I../src -I../ttmath -I$(VCFLIB_ROOT)/src/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(VCFLIB_ROOT)/fastahack/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) ++INCLUDE = -I../src -I../ttmath -I$(VCFLIB_ROOT)/src/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(VCFLIB_ROOT)/fastahack/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(TABIX_ROOT) + #INCLUDE = -I../ttmath -I$(BAMTOOLS_ROOT)/src/ -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(VCFLIB_ROOT)/fastahack/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib + + all: autoversion ../bin/freebayes ../bin/bamleftalign +@@ -46,7 +45,7 @@ + .PHONY: all static debug profiling gprof + + $(HTSLIB_ROOT)/libhts.a: +- cd $(HTSLIB_ROOT) && make ++ cd $(HTSLIB_ROOT) && make CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)" + + $(SEQLIB_ROOT)/src/libseqlib.a: + cd $(SEQLIB_ROOT) && ./configure && make +@@ -92,19 +91,19 @@ + # executables + + freebayes ../bin/freebayes: freebayes.o $(OBJECTS) $(HEADERS) $(seqlib) +- $(CXX) $(CXXFLAGS) $(INCLUDE) freebayes.o $(OBJECTS) -o ../bin/freebayes $(LIBS) ++ $(CXX) $(CXXFLAGS) $(INCLUDE) freebayes.o $(OBJECTS) -o ../bin/freebayes $(LDFLAGS) $(LIBS) + + alleles ../bin/alleles: alleles.o $(OBJECTS) $(HEADERS) $(seqlib) +- $(CXX) $(CXXFLAGS) $(INCLUDE) alleles.o $(OBJECTS) -o ../bin/alleles $(LIBS) ++ $(CXX) $(CXXFLAGS) $(INCLUDE) alleles.o $(OBJECTS) -o ../bin/alleles $(LDFLAGS) $(LIBS) + + dummy ../bin/dummy: dummy.o $(OBJECTS) $(HEADERS) $(seqlib) + $(CXX) $(CXXFLAGS) $(INCLUDE) dummy.o $(OBJECTS) -o ../bin/dummy $(LIBS) + + bamleftalign ../bin/bamleftalign: $(SEQLIB_ROOT)/src/libseqlib.a $(HTSLIB_ROOT)/libhts.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o +- $(CXX) $(CXXFLAGS) $(INCLUDE) bamleftalign.o $(OBJECTS) -o ../bin/bamleftalign $(LIBS) ++ $(CXX) $(CXXFLAGS) $(INCLUDE) bamleftalign.o $(OBJECTS) -o ../bin/bamleftalign $(LDFLAGS) $(LIBS) + + bamfiltertech ../bin/bamfiltertech: $(SEQLIB_ROOT)/src/libseqlib.a $(HTSLIB_ROOT)/libhts.a bamfiltertech.o $(OBJECTS) $(HEADERS) +- $(CXX) $(CXXFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS) ++ $(CXX) $(CXXFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LDFLAGS) $(LIBS) + + + # objects +@@ -122,7 +121,7 @@ + $(CXX) $(CXXFLAGS) $(INCLUDE) -c freebayes.cpp + + fastlz.o: fastlz.c fastlz.h +- $(C) $(CFLAGS) $(INCLUDE) -c fastlz.c ++ $(CC) $(CFLAGS) $(INCLUDE) -c fastlz.c + + Parameters.o: Parameters.cpp Parameters.h Version.h + $(CXX) $(CXXFLAGS) $(INCLUDE) -c Parameters.cpp +@@ -256,7 +255,7 @@ + autoversion: + @( \ + if [ -d "../.git" ] && which git > /dev/null ; then \ +- DETECTED_VERSION=$$(git describe --always --tags --dirty) ; \ ++ DETECTED_VERSION=$$(git describe --always --tags) ; \ + else \ + DETECTED_VERSION=$$(grep -v "^#" "$(RELEASED_VERSION_FILE)") ; \ + fi ; \ diff --git a/recipes/freebayes/1.2.0/vcflib/tabixpp/Makefile.patch b/recipes/freebayes/1.2.0/vcflib/tabixpp/Makefile.patch deleted file mode 100644 index 5eb23dc8..00000000 --- a/recipes/freebayes/1.2.0/vcflib/tabixpp/Makefile.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- vcflib/tabixpp/Makefile 2018-09-06 14:30:22.309883227 +0000 -+++ vcflib/tabixpp/Makefile.lib 2018-09-07 12:54:14.400585361 +0000 -@@ -35,7 +35,7 @@ - $(CXX) $(CXXFLAGS) -c tabix.cpp $(INCLUDES) - - htslib/libhts.a: -- cd htslib && $(MAKE) lib-static -+ cd htslib && $(MAKE) lib-static LDFLAGS="-L$(PREFIX)/lib" CPPFLAGS="-I$(PREFIX)/include" - - tabix++: tabix.o main.cpp $(HTS_LIB) - $(CXX) $(CXXFLAGS) -o $@ main.cpp tabix.o $(INCLUDES) $(LIBPATH) \ diff --git a/recipes/freebayes/1.2.0/vcflib_Makefile.patch b/recipes/freebayes/1.2.0/vcflib_Makefile.patch new file mode 100644 index 00000000..7c0b2c1c --- /dev/null +++ b/recipes/freebayes/1.2.0/vcflib_Makefile.patch @@ -0,0 +1,11 @@ +--- vcflib/Makefile 2018-10-12 08:22:31.942384685 +0100 ++++ vcflib/Makefile.1 2018-10-12 08:22:25.410359972 +0100 +@@ -136,7 +136,7 @@ + + GIT_VERSION := $(shell git describe --abbrev=4 --dirty --always) + +-CXX = g++ ++CXX ?= g++ + CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x + #CXXFLAGS = -O2 + #CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual diff --git a/recipes/freebayes/1.2.0/vcflib_tabixpp_Makefile.patch b/recipes/freebayes/1.2.0/vcflib_tabixpp_Makefile.patch new file mode 100644 index 00000000..ea546aa0 --- /dev/null +++ b/recipes/freebayes/1.2.0/vcflib_tabixpp_Makefile.patch @@ -0,0 +1,15 @@ +--- vcflib/tabixpp/Makefile 2018-10-12 09:46:11.236657824 +0100 ++++ vcflib/tabixpp/Makefile.1 2018-10-12 09:46:05.452842794 +0100 +@@ -35,10 +35,10 @@ + $(CXX) $(CXXFLAGS) -c tabix.cpp $(INCLUDES) + + htslib/libhts.a: +- cd htslib && $(MAKE) lib-static ++ cd htslib && $(MAKE) lib-static LDFLAGS="$(LDFLAGS)" CPPFLAGS="$(CPPFLAGS)" + + tabix++: tabix.o main.cpp $(HTS_LIB) +- $(CXX) $(CXXFLAGS) -o $@ main.cpp tabix.o $(INCLUDES) $(LIBPATH) \ ++ $(CXX) $(CXXFLAGS) -o $@ main.cpp tabix.o $(INCLUDES) $(LDFLAGS) $(LIBPATH) \ + -lhts -lpthread -lm -lz + + cleanlocal: diff --git a/recipes/freebayes/1.2.0/vcflib_tabixpp_htslib_Makefile.patch b/recipes/freebayes/1.2.0/vcflib_tabixpp_htslib_Makefile.patch new file mode 100644 index 00000000..b58c47e7 --- /dev/null +++ b/recipes/freebayes/1.2.0/vcflib_tabixpp_htslib_Makefile.patch @@ -0,0 +1,42 @@ +--- vcflib/tabixpp/htslib/Makefile 2018-10-12 09:24:05.167501636 +0100 ++++ vcflib/tabixpp/htslib/Makefile.1 2018-10-12 09:23:56.747337409 +0100 +@@ -22,16 +22,16 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc +-AR = ar +-RANLIB = ranlib ++CC ?= gcc ++AR ?= ar ++RANLIB ?= ranlib + + CPPFLAGS = + # TODO: probably update cram code to make it compile cleanly with -Wc++-compat +-CFLAGS = -g -Wall -O2 ++CFLAGS ?= -g -Wall -O2 + EXTRA_CFLAGS_PIC = -fpic +-LDFLAGS = +-LIBS = ++LDFLAGS ?= ++LIBS ?= + + # For now these don't work too well as samtools also needs to know to + # add -lbz2 and -llzma if linking against the static libhts.a library. +@@ -291,13 +291,13 @@ + + + bgzip: bgzip.o libhts.a +- $(CC) -pthread $(LDFLAGS) -o $@ bgzip.o libhts.a -lz $(LIBS) ++ $(CC) -pthread $(LDFLAGS) -o $@ bgzip.o libhts.a $(LDFLAGS) -lz $(LIBS) + + htsfile: htsfile.o libhts.a +- $(CC) -pthread $(LDFLAGS) -o $@ htsfile.o libhts.a -lz $(LIBS) ++ $(CC) -pthread $(LDFLAGS) -o $@ htsfile.o libhts.a $(LDFLAGS) -lz $(LIBS) + + tabix: tabix.o libhts.a +- $(CC) -pthread $(LDFLAGS) -o $@ tabix.o libhts.a -lz $(LIBS) ++ $(CC) -pthread $(LDFLAGS) -o $@ tabix.o libhts.a $(LDFLAGS) -lz $(LIBS) + + bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h) + htsfile.o: htsfile.c config.h $(htslib_hfile_h) $(htslib_hts_h) $(htslib_sam_h) $(htslib_vcf_h) diff --git a/recipes/gmplib/6.1.2/build.sh b/recipes/gmplib/6.1.2/build.sh index 763c5bc3..c47a4f91 100644 --- a/recipes/gmplib/6.1.2/build.sh +++ b/recipes/gmplib/6.1.2/build.sh @@ -1,14 +1,14 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" # -march=x86_64 and MPN_PATH are set enable a build product that is # -portable across our CPUs ./configure --prefix="$PREFIX" \ CFLAGS="-O2 -pedantic -fomit-frame-pointer -m64 -march=x86-64" \ MPN_PATH="x86_64 generic" -make -j $n +make -j $n LDFLAGS="-Wl,-rpath-link,$PREFIX/lib" make check make install prefix="$PREFIX" diff --git a/recipes/gmplib/6.1.2/meta.yaml b/recipes/gmplib/6.1.2/meta.yaml index e7a0fd07..f9d27f5f 100644 --- a/recipes/gmplib/6.1.2/meta.yaml +++ b/recipes/gmplib/6.1.2/meta.yaml @@ -11,7 +11,7 @@ about: summary: "The GNU Multiple Precision Arithmetic Library." build: - number: 1 + number: 2 source: url: https://gmplib.org/download/gmp/gmp-{{ version }}.tar.xz @@ -20,13 +20,38 @@ source: requirements: build: - - gcc_npg >=7.3 - - zlib - + - {{ compiler("c") }} run: - - zlib + - {{ pin_subpackage("libgmp-dev", exact=True) }} + +outputs: + - name: libgmp + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - m4 + - make + host: + - libz-dev + run: + - libz + files: + - lib/libgmp.a + - lib/libgmp.so* + test: + commands: + - test -f ${PREFIX}/lib/libgmp.a + - test -h ${PREFIX}/lib/libgmp.so -test: - commands: - - test -f ${PREFIX}/lib/libgmp.a - - test -f ${PREFIX}/lib/libgmp.so + - name: libgmp-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libgmp", exact=True) }} + files: + - include + - share + test: + commands: + - test -f ${PREFIX}/include/gmp.h diff --git a/recipes/gnutls/3.4.17/build.sh b/recipes/gnutls/3.4.17/build.sh index 6a610eaa..54dae1db 100644 --- a/recipes/gnutls/3.4.17/build.sh +++ b/recipes/gnutls/3.4.17/build.sh @@ -1,15 +1,17 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" ./configure --prefix="$PREFIX" \ --with-included-libtasn1 \ - --with-included-unistring \ - --with-zlib-prefix="$PREFIX" \ + --with-libz-prefix="$PREFIX" \ --without-idn \ --without-p11-kit \ --without-tpm -make -j $n + +make -j $n prefix="$PREFIX" CC="$GCC" \ + CPPFLAGS="-I$PREFIX/include" \ + LDFLAGS="-Wl,-rpath-link,$PREFIX/lib -Wl,--disable-new-dtags" make install prefix="$PREFIX" diff --git a/recipes/gnutls/3.4.17/meta.yaml b/recipes/gnutls/3.4.17/meta.yaml index 8d36215e..2fc4cae5 100644 --- a/recipes/gnutls/3.4.17/meta.yaml +++ b/recipes/gnutls/3.4.17/meta.yaml @@ -12,26 +12,78 @@ about: summary: "The GnuTLS Transport Layer Security Library." build: - number: 0 + number: 1 source: - url: https://www.gnupg.org/ftp/gcrypt/gnutls/v{{ short_version }}/gnutls-{{ version }}.tar.xz fn: gnutls-{{ version }}.tar.xz sha256: {{ sha256 }} -requirements: - build: - - gcc_npg >=7.3 - - gmplib - - nettle - - zlib +outputs: + - name: gnutls + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - libtool + - make + - pkg-config + host: + - libgmp-dev + - libnettle-dev + - libz-dev + run: + - {{ pin_subpackage("libgnutls", exact=True) }} + - libgmp + - libnettle + - libz + files: + - bin/certtool + - bin/gnutls-cli + - bin/gnutls-cli-debug + - bin/gnutls-serv + - bin/ocsptool + - bin/psktool + - bin/srptool + - share/info + - share/man/man1 + test: + commands: + - gnutls-cli -h - run: - - libgcc_npg - - gmplib - - nettle - - zlib + - name: libgnutls + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - libtool + - make + - pkg-config + host: + - libgmp-dev + - libnettle-dev + - libz-dev + run: + - libgmp + - libnettle + - libz + files: + - lib/libgnutls.* + - lib/libgnutlsxx.* + - share/locale + tests: + commands: + - test -h ${PREFIX}/lib/libgnutls.so -test: - commands: - - gnutls-cli -h + - name: libgnutls-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libgnutls", exact=True) }} + files: + - include/gnutls + - lib/pkgconfig/gnutls.pc + - man/man3 + tests: + commands: + - test -f ${PREFIX}/include/gnutls/gnutls.h diff --git a/recipes/hdf5/1.10.1/build.sh b/recipes/hdf5/1.10.1/build.sh index edd70785..f669fa27 100755 --- a/recipes/hdf5/1.10.1/build.sh +++ b/recipes/hdf5/1.10.1/build.sh @@ -1,10 +1,12 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" -./configure --prefix="$PREFIX" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +./configure --prefix="$PREFIX" \ + CPPFLAGS="-I$PREFIX/include" \ + LDFLAGS="-L$PREFIX/lib" -make -j $n +make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install prefix="$PREFIX" diff --git a/recipes/hdf5/1.10.1/meta.yaml b/recipes/hdf5/1.10.1/meta.yaml index 79fcb728..7a61420b 100644 --- a/recipes/hdf5/1.10.1/meta.yaml +++ b/recipes/hdf5/1.10.1/meta.yaml @@ -12,7 +12,7 @@ about: summary: A data model, library, and file format for storing and managing data. build: - number: 1 + number: 2 string: threadsafe_{{ PKG_BUILDNUM }} source: @@ -20,17 +20,18 @@ source: fn: hdf5-{{ version }}.tar.gz sha256: {{ sha256 }} -requirements: - build: - - gcc_npg >=7.3 - - zlib - outputs: - name: hdf5 version: {{ version }} requirements: + build: + - {{ compiler("cxx") }} + - make + host: + - libz-dev run: - - libhdf5 =={{ version }} + - {{ pin_subpackage("libhdf5", exact=True) }} + - libz files: - bin/gif2h5 - bin/h52gif @@ -54,17 +55,31 @@ outputs: - h5dump -h - name: libhdf5 + version: {{ version }} + requirements: + build: + - {{ compiler("cxx") }} + - make + host: + - libz-dev + run: + - libz + files: + - lib/libhdf* + test: + commands: + - test -f ${PREFIX}/lib/libhdf5.a + - test -h ${PREFIX}/lib/libhdf5.so + + - name: libhdf5-dev version: {{ version }} requirements: run: - - zlib + - {{ pin_subpackage("libhdf5", exact=True) }} files: - include/H5* - include/hdf5* - - lib/libhdf* - share/hdf5_examples test: commands: - test -f ${PREFIX}/include/hdf5.h - - test -f ${PREFIX}/lib/libhdf5.a - - test -h ${PREFIX}/lib/libhdf5.so diff --git a/recipes/hisat2/2.1.0/Makefile.patch b/recipes/hisat2/2.1.0/Makefile.patch new file mode 100644 index 00000000..fd7ba522 --- /dev/null +++ b/recipes/hisat2/2.1.0/Makefile.patch @@ -0,0 +1,13 @@ +--- Makefile 2018-10-08 16:47:39.624438097 +0100 ++++ Makefile.1 2018-10-08 16:49:19.511542637 +0100 +@@ -23,8 +23,8 @@ + INC = + GCC_PREFIX = $(shell dirname `which gcc`) + GCC_SUFFIX = +-CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX) +-CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX) ++CC ?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX) ++CPP ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX) + CXX = $(CPP) + HEADERS = $(wildcard *.h) + BOWTIE_MM = 1 diff --git a/recipes/hisat2/2.1.0/build.sh b/recipes/hisat2/2.1.0/build.sh index bb92d396..65cc5420 100644 --- a/recipes/hisat2/2.1.0/build.sh +++ b/recipes/hisat2/2.1.0/build.sh @@ -1,10 +1,11 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" -make -j $n +make -j $n CC="$GCC" CPP="$CXX" \ + CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" mkdir -p "$PREFIX/bin" @@ -14,4 +15,4 @@ for file in hisat2 hisat2-align-s hisat2-align-l \ hisat2_extract_splice_sites.py hisat2_extract_exons.py do cp $file "$PREFIX/bin" -done \ No newline at end of file +done diff --git a/recipes/hisat2/2.1.0/meta.yaml b/recipes/hisat2/2.1.0/meta.yaml index 0ff582d0..6a7ad08a 100644 --- a/recipes/hisat2/2.1.0/meta.yaml +++ b/recipes/hisat2/2.1.0/meta.yaml @@ -7,29 +7,26 @@ package: about: home: http://ccb.jhu.edu/software/hisat2/index.shtml - license: GPLv3 - summary: graph-based alignment of next generation sequencing reads to a population of genomes. + license: GPL3 + summary: "Graph-based alignment of next generation sequencing reads to a population of genomes." build: - number: 0 - - rpaths: - - lib64 - - lib + number: 1 source: url: ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-{{ version }}-source.zip fn: hisat2-{{ version }}-source.zip sha256: {{ sha256 }} + patches: + - Makefile.patch requirements: build: - - gcc_npg >=7.3 - - zlib - + - {{ compiler("cxx") }} + host: + - libz-dev run: - - libgcc_npg >=7.3 - - zlib + - libz test: commands: diff --git a/recipes/htslib/1.9+47-gc93b673/build.sh b/recipes/htslib/1.9+47-gc93b673/build.sh index 53756abb..c404a9d9 100755 --- a/recipes/htslib/1.9+47-gc93b673/build.sh +++ b/recipes/htslib/1.9+47-gc93b673/build.sh @@ -1,10 +1,11 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" pushd htslib + cp aclocal.m4 aclocal.m4.tmp autoreconf cp aclocal.m4.tmp aclocal.m4 @@ -18,6 +19,7 @@ make install prefix="$PREFIX" popd pushd plugins -make install prefix="$PREFIX" IRODS_HOME="$PREFIX" \ - CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make IRODS_HOME="$PREFIX" \ + CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make install prefix="$PREFIX" popd diff --git a/recipes/htslib/1.9+47-gc93b673/meta.yaml b/recipes/htslib/1.9+47-gc93b673/meta.yaml index a5f095d5..fd333e96 100644 --- a/recipes/htslib/1.9+47-gc93b673/meta.yaml +++ b/recipes/htslib/1.9+47-gc93b673/meta.yaml @@ -12,7 +12,7 @@ about: summary: C library for high-throughput sequencing data formats. build: - number: 0 + number: 1 string: plugins_{{ plugins_rev }}_{{ PKG_BUILDNUM }} source: @@ -26,27 +26,29 @@ source: features: - irods -requirements: - build: - - libbzip2 - - libcurl - - gcc_npg >=7.3 - - irods-dev >=4.1.12 # for plugins - - liblzma - - openssl - - zlib - outputs: - - name: htsbin + - name: htslib version: {{ version }} requirements: + build: + - {{ compiler("c") }} + - autoconf + - make + - perl + host: + - irods-dev >=4.1.12 + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libssl-dev + - libz-dev run: - - htslib =={{ version }} - - libbzip2 + - {{ pin_subpackage("libhts", exact=True) }} + - libbz2 - libcurl - liblzma - - openssl - - zlib + - libssl + - libz files: - bin/bgzip - bin/htsfile @@ -54,27 +56,46 @@ outputs: - share/man/man1/htsfile.1 - share/man/man1/tabix.1 - - name: htslib + - name: libhts version: {{ version }} requirements: + build: + - {{ compiler("c") }} + - autoconf + - make + host: + - irods-dev >=4.1.12 + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libssl-dev + - libz-dev run: - - libbzip2 + - libbz2 - libcurl - liblzma - - openssl - - zlib + - libssl + - libz files: - - include/htslib - libexec/htslib - lib/libhts* - - share/man/man5/faidx.5 - - share/man/man5/sam.5 - - share/man/man5/vcf.5 - test: commands: - - test -f ${PREFIX}/include/htslib/sam.h - test -f ${PREFIX}/lib/libhts.a - test -h ${PREFIX}/lib/libhts.so - test -f ${PREFIX}/libexec/htslib/hfile_irods.so - test -f ${PREFIX}/libexec/htslib/hfile_libcurl.so + + - name: libhts-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libhts", exact=True) }} + files: + - include/htslib + - share/man/man5/faidx.5 + - share/man/man5/sam.5 + - share/man/man5/vcf.5 + test: + commands: + - test -f ${PREFIX}/include/htslib/sam.h diff --git a/recipes/htslib/1.9+9-g6ec3b94/build.sh b/recipes/htslib/1.9+9-g6ec3b94/build.sh index 45df1b01..c404a9d9 100755 --- a/recipes/htslib/1.9+9-g6ec3b94/build.sh +++ b/recipes/htslib/1.9+9-g6ec3b94/build.sh @@ -1,8 +1,8 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" pushd htslib @@ -19,6 +19,7 @@ make install prefix="$PREFIX" popd pushd plugins -make install prefix="$PREFIX" IRODS_HOME="$PREFIX" \ - CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make IRODS_HOME="$PREFIX" \ + CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make install prefix="$PREFIX" popd diff --git a/recipes/htslib/1.9+9-g6ec3b94/meta.yaml b/recipes/htslib/1.9+9-g6ec3b94/meta.yaml index 19051a3f..f4512158 100644 --- a/recipes/htslib/1.9+9-g6ec3b94/meta.yaml +++ b/recipes/htslib/1.9+9-g6ec3b94/meta.yaml @@ -12,7 +12,7 @@ about: summary: C library for high-throughput sequencing data formats. build: - number: 1 + number: 2 string: plugins_{{ plugins_rev }}_{{ PKG_BUILDNUM }} source: @@ -26,27 +26,29 @@ source: features: - irods -requirements: - build: - - libbzip2 - - libcurl - - gcc_npg >=7.3 - - irods-dev >=4.1.12 # for plugins - - liblzma - - openssl - - zlib - outputs: - - name: htsbin + - name: htslib version: {{ version }} requirements: + build: + - {{ compiler("c") }} + - autoconf + - make + - perl + host: + - irods-dev >=4.1.12 + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libssl-dev + - libz-dev run: - - htslib =={{ version }} - - libbzip2 + - {{ pin_subpackage("libhts", exact=True) }} + - libbz2 - libcurl - liblzma - - openssl - - zlib + - libssl + - libz files: - bin/bgzip - bin/htsfile @@ -54,27 +56,46 @@ outputs: - share/man/man1/htsfile.1 - share/man/man1/tabix.1 - - name: htslib + - name: libhts version: {{ version }} requirements: + build: + - {{ compiler("c") }} + - autoconf + - make + host: + - irods-dev >=4.1.12 + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libssl-dev + - libz-dev run: - - libbzip2 + - libbz2 - libcurl - liblzma - - openssl - - zlib + - libssl + - libz files: - - include/htslib - libexec/htslib - lib/libhts* - - share/man/man5/faidx.5 - - share/man/man5/sam.5 - - share/man/man5/vcf.5 - test: commands: - - test -f ${PREFIX}/include/htslib/sam.h - test -f ${PREFIX}/lib/libhts.a - test -h ${PREFIX}/lib/libhts.so - test -f ${PREFIX}/libexec/htslib/hfile_irods.so - test -f ${PREFIX}/libexec/htslib/hfile_libcurl.so + + - name: libhts-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libhts", exact=True) }} + files: + - include/htslib + - share/man/man5/faidx.5 + - share/man/man5/sam.5 + - share/man/man5/vcf.5 + test: + commands: + - test -f ${PREFIX}/include/htslib/sam.h diff --git a/recipes/irods/4.1.12/build.sh b/recipes/irods/4.1.12/build.sh index 8a4b0772..df2a1b78 100644 --- a/recipes/irods/4.1.12/build.sh +++ b/recipes/irods/4.1.12/build.sh @@ -2,7 +2,6 @@ set -e - function untar_data() { if [ -e data.tar.gz ]; then tar xz --strip-components=2 --directory="$PREFIX" --exclude='*.o' --exclude-backups < data.tar.gz @@ -11,11 +10,25 @@ function untar_data() { fi } +export TERM=dumb + git submodule init && git submodule update -export CCFLAGS="-I$PREFIX/include" -export LDFLAGS="-L$PREFIX/lib" -export TERM=dumb +sudo apt-get install -y g++ g++-4.8 gcc gcc-4.8 + +sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 100 +sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 100 +sudo update-alternatives --set gcc /usr/bin/gcc-4.8 +sudo update-alternatives --set g++ /usr/bin/g++-4.8 + +sudo apt-get install -y autoconf automake help2man make \ + libtool-bin pkg-config texinfo + +sudo apt-get install -y libjson-perl python-dev + +sudo apt-get install -y libbz2-dev libcurl4-gnutls-dev \ + libfuse-dev libkrb5-dev libmysqlclient-dev libpam0g-dev \ + libssl-dev unixodbc-dev libxml2-dev zlib1g-dev ./packaging/build.sh --verbose icat postgres ./packaging/build.sh --verbose icommands diff --git a/recipes/irods/4.1.12/conda_build_config.yaml b/recipes/irods/4.1.12/conda_build_config.yaml new file mode 100644 index 00000000..15150c0f --- /dev/null +++ b/recipes/irods/4.1.12/conda_build_config.yaml @@ -0,0 +1,6 @@ +c_compiler_version: + - 5.4 + +cxx_compiler_version: + - 5.4 + diff --git a/recipes/irods/4.1.12/meta.yaml b/recipes/irods/4.1.12/meta.yaml index 604bd6d0..797f9056 100644 --- a/recipes/irods/4.1.12/meta.yaml +++ b/recipes/irods/4.1.12/meta.yaml @@ -10,28 +10,12 @@ about: summary: "Open Source Data Management Software." build: - number: 0 - - rpaths: - - lib64 - - lib + number: 1 source: git_url: https://github.com/irods/irods.git git_rev: 4-1-stable - patches: - - irods.patch - -requirements: - build: - - gcc_npg ==4.6.4 - - libbzip2 - - libcurl - - libxml2 - - openssl - - zlib - outputs: - name: irods-plugins version: {{ version }} @@ -42,13 +26,7 @@ outputs: version: {{ version }} requirements: run: - - irods-plugins =={{ version }} - - libbzip2 - - libcurl - - libgcc_npg >=4.6 - - libxml2 - - openssl - - zlib + - {{ pin_subpackage("irods-plugins", exact=True) }} files: - include/irods - lib/irods/externals @@ -65,13 +43,7 @@ outputs: version: {{ version }} requirements: run: - - irods-plugins =={{ version }} - - libbzip2 - - libcurl - - libgcc_npg >=4.6 - - libxml2 - - openssl - - zlib + - {{ pin_subpackage("irods-plugins", exact=True) }} files: - bin/iadmin - bin/ibun diff --git a/recipes/jansson/2.1.0/build.sh b/recipes/jansson/2.1.0/build.sh index 37ba6066..2b038685 100755 --- a/recipes/jansson/2.1.0/build.sh +++ b/recipes/jansson/2.1.0/build.sh @@ -1,11 +1,15 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" autoreconf -fi -./configure --prefix=$PREFIX +./configure --prefix="$PREFIX" \ + CPPFLAGS="-I$PREFIX/include" \ + LDFLAGS="-L$PREFIX/lib" + +make -j $n CPPFLAGS="-I$PREFIX/include" \ + LDFLAGS="-Wl,--disable-new-dtags -L$PREFIX/lib" +make install prefix="$PREFIX" -make -j $n -make install prefix=$PREFIX diff --git a/recipes/jansson/2.1.0/meta.yaml b/recipes/jansson/2.1.0/meta.yaml index fd0d2efc..130d60d3 100644 --- a/recipes/jansson/2.1.0/meta.yaml +++ b/recipes/jansson/2.1.0/meta.yaml @@ -2,7 +2,7 @@ {% set sha256 = "b0a899f90ade82e42da0ecabc8af1fa296d69691e7c0786c4994fb79d4833ebb" %} package: - name: jansson + name: libjansson version: "{{ version }}" about: @@ -15,12 +15,34 @@ source: fn: jansson-{{ version }}.tar.gz sha256: {{ sha256 }} -requirements: - build: - - gcc_npg >=7.3 +build: + number: 1 -test: - commands: - - test -f ${PREFIX}/include/jansson.h - - test -f ${PREFIX}/lib/libjansson.a - - test -h ${PREFIX}/lib/libjansson.so +outputs: + - name: libjansson + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + - libtool + - make + - perl + files: + - lib/libjansson.* + test: + commands: + - test -f ${PREFIX}/lib/libjansson.a + - test -h ${PREFIX}/lib/libjansson.so + + - name: libjansson-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libjansson", exact=True) }} + files: + - include/jansson*.h + - lib/pkgconfig/jansson.pc + test: + commands: + - test -f ${PREFIX}/include/jansson.h diff --git a/recipes/jq/1.5/build.sh b/recipes/jq/1.5/build.sh index d6faf8bc..52f67cc4 100755 --- a/recipes/jq/1.5/build.sh +++ b/recipes/jq/1.5/build.sh @@ -1,8 +1,8 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" ./configure --prefix="$PREFIX" --disable-maintainer-mode diff --git a/recipes/jq/1.5/meta.yaml b/recipes/jq/1.5/meta.yaml index 4fa27c36..d4cec4ac 100644 --- a/recipes/jq/1.5/meta.yaml +++ b/recipes/jq/1.5/meta.yaml @@ -11,7 +11,7 @@ about: summary: "Command-line JSON processor." build: - number: 0 + number: 1 source: url: https://github.com/stedolan/jq/releases/download/jq-{{ version }}/jq-{{ version }}.tar.gz @@ -20,7 +20,8 @@ source: requirements: build: - - gcc_npg >=7.3 + - {{ compiler("c") }} + - make test: commands: diff --git a/recipes/libgd/2.2.5/build.sh b/recipes/libgd/2.2.5/build.sh index f9c7bde3..b93b9b98 100644 --- a/recipes/libgd/2.2.5/build.sh +++ b/recipes/libgd/2.2.5/build.sh @@ -1,8 +1,8 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" ./configure --prefix="$PREFIX" \ --without-fontconfig \ @@ -12,7 +12,8 @@ n=`expr $CPU_COUNT / 4 \| 1` --with-png \ --without-tiff \ --without-webp \ - --without-xpm + --without-xpm \ + --with-zlib -make -j $n +make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX" make install prefix="$PREFIX" diff --git a/recipes/libgd/2.2.5/meta.yaml b/recipes/libgd/2.2.5/meta.yaml index c0805336..a85b9475 100644 --- a/recipes/libgd/2.2.5/meta.yaml +++ b/recipes/libgd/2.2.5/meta.yaml @@ -16,20 +16,58 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 -requirements: - build: - - gcc_npg >=7.3 - - libpng - - zlib +outputs: + - name: libgd-bin + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - libtool + - pkg-config + host: + - libpng-dev + - libz-dev + run: + - {{ pin_subpackage("libgd", exact=True) }} + - libpng + - libz + files: + - bin/*gd* + - bin/*png* + test: + commands: + - test -x ${PREFIX}/bin/gdtopng - run: - - libpng - - zlib + - name: libgd + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - libtool + - pkg-config + host: + - libpng-dev + - libz-dev + run: + - libpng + - libz + files: + - lib/libgd.* + test: + commands: + - test -f ${PREFIX}/lib/libgd.a + - test -h ${PREFIX}/lib/libgd.so -test: - commands: - - test -f ${PREFIX}/include/gd.h - - test -f ${PREFIX}/lib/libgd.a - - test -h ${PREFIX}/lib/libgd.so + - name: libgd-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libgd", exact=True) }} + files: + - include + - lib/pkgconfig/gdlib.pc + test: + commands: + - test -f ${PREFIX}/include/gd.h diff --git a/recipes/libmaus2/2.0.420/build.sh b/recipes/libmaus2/2.0.420/build.sh index 4914c5f8..b71af90b 100755 --- a/recipes/libmaus2/2.0.420/build.sh +++ b/recipes/libmaus2/2.0.420/build.sh @@ -1,10 +1,18 @@ #!/bin/sh -set -e +set -ex -n=$CPU_COUNT +n="$CPU_COUNT" -./configure --prefix="$PREFIX" --with-gnutls --with-nettle --with-io_lib --with-irods=yes CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib -L$PREFIX/lib/irods/externals" LIBS="-lirods_client_api -lrt" +./configure --prefix="$PREFIX" \ + --with-gnutls \ + --with-nettle \ + --with-io_lib \ + --with-irods=yes \ + CPPFLAGS="-I$PREFIX/include" \ + LDFLAGS="-L$PREFIX/lib -L$PREFIX/lib/irods/externals" \ + LIBS="-lirods_client_api -lrt" -make -j $n +make -j $n CPPFLAGS="-I$PREFIX/include" \ + LDFLAGS="-Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib/irods/externals" make install prefix="$PREFIX" diff --git a/recipes/libmaus2/2.0.420/meta.yaml b/recipes/libmaus2/2.0.420/meta.yaml index 549ebb5d..87453aa3 100644 --- a/recipes/libmaus2/2.0.420/meta.yaml +++ b/recipes/libmaus2/2.0.420/meta.yaml @@ -11,36 +11,49 @@ about: summary: Collection of data structures and algorithms. build: - number: 0 - - rpaths: - - lib64 - - lib + number: 1 source: url: https://github.com/gt1/libmaus2/archive/{{ version }}-release-20171116172420.tar.gz fn: libmaus2-{{ version }}.tar.gz sha256: {{ sha256 }} -features: - - irods - -requirements: - build: - - gcc_npg >=7.3 - - irods-dev - - nettle - - staden_io_lib - - zlib - - run: - - libgcc_npg >=7.3 - - nettle - - staden_io_lib - - zlib +outputs: + - name: libmaus2 + version: {{ version }} + requirements: + build: + - {{ compiler("cxx") }} + - make + - pkg-config + host: + - irods-dev + - libgnutls-dev + - libnettle-dev + - libstaden-read-dev + - libz-dev + run: + - libgnutls + - libnettle + - libstaden-read + - libz + files: + - lib/libmaus*.* + - lib/libmaus2/{{ version }}/*.so + test: + commands: + - test -f ${PREFIX}/lib/libmaus2.a + - test -h ${PREFIX}/lib/libmaus2.so + + - name: libmaus2-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libmaus2", exact=True) }} + files: + - include/libmaus2 + - lib/pkgconfig/libmaus2*.pc + test: + commands: + - test -f ${PREFIX}/include/libmaus2/LibMausConfig.hpp -test: - commands: - - test -f ${PREFIX}/include/libmaus2/LibMausConfig.hpp - - test -f ${PREFIX}/lib/libmaus2.a - - test -h ${PREFIX}/lib/libmaus2.so diff --git a/recipes/libpng/1.6.34/build.sh b/recipes/libpng/1.6.34/build.sh new file mode 100644 index 00000000..f669fa27 --- /dev/null +++ b/recipes/libpng/1.6.34/build.sh @@ -0,0 +1,12 @@ +#!/bin/sh + +set -ex + +n="$CPU_COUNT" + +./configure --prefix="$PREFIX" \ + CPPFLAGS="-I$PREFIX/include" \ + LDFLAGS="-L$PREFIX/lib" + +make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make install prefix="$PREFIX" diff --git a/recipes/libpng/1.6.34/meta.yaml b/recipes/libpng/1.6.34/meta.yaml new file mode 100644 index 00000000..ed02d6a4 --- /dev/null +++ b/recipes/libpng/1.6.34/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.6.34" %} +{% set sha256 = "574623a4901a9969080ab4a2df9437026c8a87150dfd5c235e28c94b212964a7" %} + +package: + name: libpng + version: "{{ version }}" + +about: + home: http://libpng.org/pub/png/libpng.html + license: libpng + summary: "The official PNG reference library." + +source: + url: https://download.sourceforge.net/libpng/libpng-{{ version }}.tar.gz + fn: libpng-{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 1 + +outputs: + - name: libpng + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - libtool + - make + - pkg-config + host: + - libz-dev + run: + - libz + files: + - lib/libpng*.* + test: + commands: + - test -h ${PREFIX}/lib/libpng.a + - test -h ${PREFIX}/lib/libpng.so + + - name: libpng-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libpng", exact=True) }} + files: + - include + - lib/pkgconfig/libpng*.pc + - share/man + test: + commands: + - test -f ${PREFIX}/include/png.h + diff --git a/recipes/libpng/build.sh b/recipes/libpng/build.sh deleted file mode 100644 index edd70785..00000000 --- a/recipes/libpng/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/sh - -set -e - -n=`expr $CPU_COUNT / 4 \| 1` - -./configure --prefix="$PREFIX" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" - -make -j $n -make install prefix="$PREFIX" diff --git a/recipes/libpng/meta.yaml b/recipes/libpng/meta.yaml deleted file mode 100644 index f37ba590..00000000 --- a/recipes/libpng/meta.yaml +++ /dev/null @@ -1,33 +0,0 @@ -{% set version = "1.6.34" %} -{% set sha256 = "574623a4901a9969080ab4a2df9437026c8a87150dfd5c235e28c94b212964a7" %} - -package: - name: libpng - version: "{{ version }}" - -about: - home: http://libpng.org/pub/png/libpng.html - license: libpng - summary: "The official PNG reference library." - -source: - url: https://download.sourceforge.net/libpng/libpng-{{ version }}.tar.gz - fn: libpng-{{ version }}.tar.gz - sha256: {{ sha256 }} - -build: - number: 0 - -requirements: - build: - - gcc_npg >=7.3 - - zlib - - run: - - zlib - -test: - commands: - - test -f ${PREFIX}/include/png.h - - test -f ${PREFIX}/lib/libpng.a - - test -h ${PREFIX}/lib/libpng.so diff --git a/recipes/libxml2/2.9.7/build.sh b/recipes/libxml2/2.9.7/build.sh index 168a10d7..6bd4ca82 100644 --- a/recipes/libxml2/2.9.7/build.sh +++ b/recipes/libxml2/2.9.7/build.sh @@ -1,10 +1,10 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" ./configure prefix="$PREFIX" --without-python -make -j $n +make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install diff --git a/recipes/libxml2/2.9.7/meta.yaml b/recipes/libxml2/2.9.7/meta.yaml index 8734f511..ab1c15da 100644 --- a/recipes/libxml2/2.9.7/meta.yaml +++ b/recipes/libxml2/2.9.7/meta.yaml @@ -11,25 +11,63 @@ about: summary: "XML C parser and toolkit developed for the Gnome project." build: - number: 2 + number: 3 source: url: ftp://xmlsoft.org/libxml2/libxml2-{{ version }}.tar.gz fn: libxml2-{{ version }}.tar.gz sha256: {{ sha256 }} -requirements: - build: - - gcc_npg >=7.3 - - liblzma - - zlib +outputs: + - name: libxml2-bin + requirements: + build: + - {{ compiler("c") }} + - make + host: + - liblzma-dev + - libz-dev + run: + - {{ pin_subpackage('libxml2', exact=True) }} + - liblzma + - libz + files: + - bin/xml2-config + - bin/xmlcatalog + - bin/xmllint + test: + commands: + - test -f ${PREFIX}/lib/libxml2.a + - test -h ${PREFIX}/lib/libxml2.so - run: - - liblzma - - zlib + - name: libxml2 + requirements: + build: + - {{ compiler("c") }} + - make + host: + - liblzma-dev + - libz-dev + run: + - liblzma + - libz + files: + - lib/libxml2.* + test: + commands: + - test -f ${PREFIX}/lib/libxml2.a + - test -h ${PREFIX}/lib/libxml2.so -test: - commands: - - test -f ${PREFIX}/include/libxml2/libxml/uri.h - - test -f ${PREFIX}/lib/libxml2.a - - test -h ${PREFIX}/lib/libxml2.so + - name: libxml2-dev + requirements: + run: + {{ pin_subpackage('libxml2', exact=True) }} + files: + - include/libxml2 + - lib/xml2Conf.sh + - lib/pkgconfig/libxml-2.0.pc + - share/doc/libxml2-{{ version }} + - share/gtk-doc/html/libxml2 + test: + commands: + - test -f ${PREFIX}/include/libxml2/libxml/uri.h diff --git a/recipes/libxslt/1.1.32/build.sh b/recipes/libxslt/1.1.32/build.sh index fe8a7635..46c7ff8d 100644 --- a/recipes/libxslt/1.1.32/build.sh +++ b/recipes/libxslt/1.1.32/build.sh @@ -1,10 +1,10 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" ./configure prefix="$PREFIX" -make -j $n +make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install diff --git a/recipes/libxslt/1.1.32/meta.yaml b/recipes/libxslt/1.1.32/meta.yaml index dc84c675..ba35bd0a 100644 --- a/recipes/libxslt/1.1.32/meta.yaml +++ b/recipes/libxslt/1.1.32/meta.yaml @@ -11,27 +11,64 @@ about: summary: "XSLT C library developed for the GNOME project." build: - number: 0 + number: 1 source: url: ftp://xmlsoft.org/libxslt/libxslt-{{ version }}.tar.gz fn: libxslt-{{ version }}.tar.gz sha256: {{ sha256 }} -requirements: - build: - - gcc_npg >=7.3 - - libxml2 >={{ version }} - - zlib +outputs: + - name: libxslt-bin + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - make + host: + - liblzma-dev + - libxml2-dev + - libz-dev + run: + - {{ pin_subpackage("libxslt", exact=True) }} + - liblzma + - libxml2 + - libz + files: + - bin/xsltproc + test: + commands: + - xsltproc --version - run: - - libxml2 >={{ version }} - - liblzma - - zlib - -test: - commands: - - xsltproc --version - - test -f ${PREFIX}/include/libxslt/xslt.h - - test -f ${PREFIX}/lib/libxslt.a - - test -h ${PREFIX}/lib/libxslt.so + - name: libxslt + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - make + host: + - liblzma-dev + - libxml2-dev + - libz-dev + run: + - liblzma + - libxml2 + - libz + files: + - lib/libxslt.* + test: + commands: + - test -f ${PREFIX}/lib/libxslt.a + - test -h ${PREFIX}/lib/libxslt.so + + - name: libxslt-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libxslt", exact=True) }} + files: + - bin/xslt-config + - include/libxslt + test: + commands: + - test -f ${PREFIX}/include/libxslt/xslt.h diff --git a/recipes/minimap2/2.10/build.sh b/recipes/minimap2/2.10/build.sh index e7f8dbea..5934f969 100755 --- a/recipes/minimap2/2.10/build.sh +++ b/recipes/minimap2/2.10/build.sh @@ -1,10 +1,10 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" -make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make -j $n CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" mkdir -p "$PREFIX/bin" cp minimap2 "$PREFIX/bin/" diff --git a/recipes/minimap2/2.10/meta.yaml b/recipes/minimap2/2.10/meta.yaml index 9ab60db2..cfd40f30 100644 --- a/recipes/minimap2/2.10/meta.yaml +++ b/recipes/minimap2/2.10/meta.yaml @@ -11,22 +11,21 @@ about: summary: "A versatile pairwise aligner for genomic and spliced nucleotide sequences." build: - number: 1 + number: 2 source: url: https://github.com/lh3/minimap2/releases/download/v{{ version }}/minimap2-{{ version }}.tar.bz2 sha256: {{ sha256 }} - patches: - Makefile.patch requirements: build: - - gcc_npg >=7.3 - - zlib - + - {{ compiler("c") }} + host: + - libz-dev run: - - zlib + - libz test: commands: diff --git a/recipes/nanopolish/0.10.2/build.sh b/recipes/nanopolish/0.10.2/build.sh new file mode 100755 index 00000000..de1a5668 --- /dev/null +++ b/recipes/nanopolish/0.10.2/build.sh @@ -0,0 +1,14 @@ +#!/bin/sh + +set -ex + +git submodule update --init --recursive + +make EIGEN=noinstall HDF5=noinstall HTS=noinstall \ + CXXFLAGS="-I$PREFIX/include -I$PREFIX/include/eigen3" \ + LDFLAGS="-L$PREFIX/lib" LIBS="-lgomp -lhdf5 -lhts -lz" + +# There is no install target in the Makefile +mkdir -p "$PREFIX/bin" + +cp nanopolish "$PREFIX/bin/" diff --git a/recipes/nanopolish/0.10.2/meta.yaml b/recipes/nanopolish/0.10.2/meta.yaml new file mode 100644 index 00000000..a1425fb2 --- /dev/null +++ b/recipes/nanopolish/0.10.2/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.10.2" %} + +package: + name: nanopolish + version: "{{ version }}" + +about: + home: https://github.com/jts/nanopolish + license: MIT + summary: "Software package for signal-level analysis of Oxford Nanopore sequencing data." + +build: + number: 0 + +source: + git_url: https://github.com/jts/nanopolish.git + git_rev: v{{ version }} + +requirements: + build: + - {{ compiler("cxx") }} + - make + host: + - eigen + - libhdf5-dev + - libbz2-dev + - libhts-dev + - liblzma-dev + - libz-dev + run: + - libbz2 + - libhdf5 + - libhts + - liblzma + - libz diff --git a/recipes/nettle/3.3/build.sh b/recipes/nettle/3.3/build.sh index d35d87b3..b8d2e1b5 100755 --- a/recipes/nettle/3.3/build.sh +++ b/recipes/nettle/3.3/build.sh @@ -1,10 +1,12 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" -./configure --prefix="$PREFIX" +./configure --prefix="$PREFIX" \ + --with-include-path="$PREFIX/include" \ + --with-lib-path="$PREFIX/lib" -make -j $n +make -j $n LDFLAGS="-Wl,-rpath-link,$PREFIX/lib -Wl,--disable-new-dtags -L$PREFIX/lib" make install prefix="$PREFIX" diff --git a/recipes/nettle/3.3/meta.yaml b/recipes/nettle/3.3/meta.yaml index f47deaa5..76c98cd3 100644 --- a/recipes/nettle/3.3/meta.yaml +++ b/recipes/nettle/3.3/meta.yaml @@ -7,26 +7,73 @@ package: about: home: https://www.lysator.liu.se/~nisse/nettle/ - license: GPL2 + license: GPL2 summary: A low-level cryptographic library build: - number: 1 + number: 2 source: url: https://ftp.gnu.org/gnu/nettle/nettle-{{ version }}.tar.gz fn: nettle-{{ version }}.tar.gz sha256: {{ sha256 }} -requirements: - build: - - gcc_npg >=7.3 - - gmplib >=5.0 +outputs: + - name: nettle + requirements: + build: + - {{ compiler("c") }} + - libtool + - m4 + - make + - pkg-config + host: + - libgmp-dev >=6.0 + run: + - {{ pin_subpackage("libnettle", exact=True) }} + - libgmp >=6.0 + files: + - bin/nettle-hash + - bin/nettle-lfib-stream + - bin/nettle-pbkdf2 + - bin/pkcs1-conv + - bin/sexp-conv + test: + commands: + - nettle-hash --help -test: - commands: - - test -f ${PREFIX}/include/nettle/sha1.h - - test -f ${PREFIX}/lib/libnettle.a - - test -h ${PREFIX}/lib/libnettle.so - - test -f ${PREFIX}/lib/libhogweed.a - - test -h ${PREFIX}/lib/libhogweed.so + - name: libnettle + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - libtool + - m4 + - make + - pkg-config + host: + - libgmp-dev >=6.0 + run: + - libgmp >=6.0 + files: + - lib/libhogweed.* + - lib/libnettle.* + test: + commands: + - test -f ${PREFIX}/lib/libnettle.a + - test -h ${PREFIX}/lib/libnettle.so + - test -f ${PREFIX}/lib/libhogweed.a + - test -h ${PREFIX}/lib/libhogweed.so + + - name: libnettle-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libnettle", exact=True) }} + files: + - include/nettle + - lib/pkgconfig/hogweed.pc + - lib/pkgconfig/nettle.pc + test: + commands: + - test -f ${PREFIX}/include/nettle/sha1.h diff --git a/recipes/npg_qc_utils/65.0/build.sh b/recipes/npg_qc_utils/65.0/build.sh index 5458e425..c57e7461 100755 --- a/recipes/npg_qc_utils/65.0/build.sh +++ b/recipes/npg_qc_utils/65.0/build.sh @@ -1,38 +1,42 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` - -pushd samtools -./configure --prefix="$PREFIX" --without-curses -make -j $n CFLAGS="-fPIC" -ln -s . include -popd +n="$CPU_COUNT" pushd npg_qc_utils pushd fastq_summ mkdir -p build -make -j $n INCLUDES="-I. -I$SRC_DIR/samtools -I$PREFIX/include" SAMTOOLSLIBPATH="-L$SRC_DIR/samtools -L$PREFIX/lib" LIBS="-lz -lm" +make -j $n CC="$GCC" \ + INCLUDES="-I. -I$PREFIX/include/samtools -I$PREFIX/include" \ + SAMTOOLSLIBPATH="-L$PREFIX/lib" \ + LIBS="-lz -lm" make install installdir="$PREFIX/bin/" popd pushd fastqcheck mkdir -p build -make -j $n INCLUDES="-I. -I$SRC_DIR/samtools -I$PREFIX/include" SAMTOOLSLIBPATH="-L$SRC_DIR/samtools -L$PREFIX/lib" LIBS="-lz -lm" +make -j $n CC="$GCC" \ + INCLUDES="-I. -I$PREFIX/include/samtools -I$PREFIX/include" \ + SAMTOOLSLIBPATH="-L$PREFIX/lib" \ + LIBS="-lz -lm" make install installdir="$PREFIX/bin/" popd pushd norm_fit mkdir -p build -make -j $n INCLUDES="-I. -I$PREFIX/include" LIBPATH="-L$PREFIX/lib" +make -j $n CC="$GCC" \ + INCLUDES="-I.-I$PREFIX/include/samtools -I$PREFIX/include" \ + LIBPATH="-L$PREFIX/lib" cp ./build/norm_fit "$PREFIX/bin/" popd pushd gt_utils mkdir -p build -make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make -j $n CC="$GCC" \ + CPPFLAGS="-I$PREFIX/include" \ + LDFLAGS="-L$PREFIX/lib" make install installdir="$PREFIX/bin" popd diff --git a/recipes/npg_qc_utils/65.0/meta.yaml b/recipes/npg_qc_utils/65.0/meta.yaml index ee7a2d8d..12dc5527 100644 --- a/recipes/npg_qc_utils/65.0/meta.yaml +++ b/recipes/npg_qc_utils/65.0/meta.yaml @@ -1,8 +1,5 @@ {% set version = "65.0" %} -{% set samtools_version = "1.8" %} -{% set samtools_sha256 = "c942bc1d9b85fd1b05ea79c5afd2805d489cd36b2c2d8517462682a4d779be16" %} - package: name: npg_qc_utils version: "{{ version }}" @@ -13,27 +10,23 @@ about: summary: "C programs extracted from npg_qc." build: - number: 4 + number: 5 source: - - url: https://sourceforge.net/projects/samtools/files/samtools/{{ samtools_version }}/samtools-{{ samtools_version }}.tar.bz2/download - fn: samtools-{{ samtools_version }}.tar.bz2 - folder: samtools - sha256: {{ samtools_sha256 }} - - git_url: https://github.com/wtsi-npg/npg_qc_utils.git git_rev: {{ version }} - folder: npg_qc_utils requirements: build: - - gcc_npg >=7.3 - - htslib <1.9 - - zlib - + - {{ compiler("c") }} + - make + host: + - libhts-dev + - samtools-dev + - libz-dev run: - - htslib <1.9 - - zlib + - libhts + - libz test: commands: diff --git a/recipes/openssl/1.0.2o/build.sh b/recipes/openssl/1.0.2o/build.sh index 34cd6a9f..66128374 100644 --- a/recipes/openssl/1.0.2o/build.sh +++ b/recipes/openssl/1.0.2o/build.sh @@ -1,8 +1,8 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" ./config --prefix="$PREFIX" \ --libdir=lib \ @@ -11,5 +11,6 @@ n=`expr $CPU_COUNT / 4 \| 1` --with-zlib-lib="$PREFIX/lib" \ shared zlib-dynamic -make -j $n +make -j $n CC="$GCC" \ + LDFLAGS="-Wl,-rpath-link,$PREFIX/lib -Wl,--disable-new-dtags" make install prefix="$PREFIX" diff --git a/recipes/openssl/1.0.2o/meta.yaml b/recipes/openssl/1.0.2o/meta.yaml index ef441349..90cde470 100644 --- a/recipes/openssl/1.0.2o/meta.yaml +++ b/recipes/openssl/1.0.2o/meta.yaml @@ -11,23 +11,57 @@ about: summary: "Cryptography and SSL/TLS Toolkit." build: - number: 0 + number: 1 source: - url: https://www.openssl.org/source/openssl-{{ version }}.tar.gz fn: openssl-{{ version }}.tar.gz sha256: {{ sha256 }} -requirements: - build: - - gcc_npg >=7.3 - - zlib - - runn: - - zlib - -test: - commands: - - openssl s_client -CApath /etc/ssl/certs/ -connect www.sanger.ac.uk:443 +outputs: + - name: openssl + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - libtool + - make + - pkg-config + host: + - libz-dev + run: + - {{ pin_subpackage("libssl", exact=True) }} + - libz + files: + - bin/c_rehash + - bin/openssl + - etc/ssl/man/man1 + test: + commands: + - openssl s_client -CApath /etc/ssl/certs/ -connect www.sanger.ac.uk:443 + - name: libssl + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - libtool + - make + - pkg-config + host: + - libz-dev + run: + - libz + files: + - lib/libcrypto.* + - lib/libssl.* + - lib/engines + - name: libssl-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libssl", exact=True) }} + files: + - etc/ssl/man/man3 + - include/openssl diff --git a/recipes/pcre/8.41/build.sh b/recipes/pcre/8.41/build.sh index fce1f273..3c92a411 100644 --- a/recipes/pcre/8.41/build.sh +++ b/recipes/pcre/8.41/build.sh @@ -1,9 +1,10 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" -./configure prefix="$PREFIX" -make -j $n +./configure prefix="$PREFIX" \ + CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install diff --git a/recipes/pcre/8.41/meta.yaml b/recipes/pcre/8.41/meta.yaml index 2480aad2..d4272336 100644 --- a/recipes/pcre/8.41/meta.yaml +++ b/recipes/pcre/8.41/meta.yaml @@ -11,28 +11,68 @@ about: summary: "Perl Compatible Regular Expressions." build: - number: 2 + number: 3 source: url: https://ftp.pcre.org/pub/pcre/pcre-{{ version }}.tar.gz fn: pcre-{{ version }}.tar.gz sha256: {{ sha256 }} -requirements: - build: - - libbzip2 - - gcc_npg >=7.3 - - liblzma - - zlib +outputs: + - name: pcre + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - {{ compiler("cxx") }} + - make + host: + - libbz2-dev + - liblzma-dev + - libz-dev + run: + - {{ pin_subpackage("libpcre", exact=True) }} + - libbz2 + - liblzma + - libz + files: + - bin/pcregrep + - bin/pcretest + test: + commands: + - pcregrep --help - run: - - libbzip2 - - libgcc_npg >=7.3 - - liblzma - - zlib + - name: libpcre + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - {{ compiler("cxx") }} + - make + host: + - libbz2-dev + - liblzma-dev + - libz-dev + run: + - libbz2 + - liblzma + - libz + files: + - lib/libpcre*.* + test: + commands: + - test -f ${PREFIX}/lib/libpcre.a + - test -h ${PREFIX}/lib/libpcre.so -test: - commands: - - test -f ${PREFIX}/include/pcre.h - - test -f ${PREFIX}/lib/libpcre.a - - test -h ${PREFIX}/lib/libpcre.so + - name: libpcre-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libpcre", exact=True) }} + files: + - bin/pcre-config + - include/pcre*.h + - lib/pkgconfig/libpcre*.pc + test: + commands: + - test -f ${PREFIX}/include/pcre.h diff --git a/recipes/python-magic/0.4.15/meta.yaml b/recipes/python-magic/0.4.15/meta.yaml index ff69145f..49486f3d 100644 --- a/recipes/python-magic/0.4.15/meta.yaml +++ b/recipes/python-magic/0.4.15/meta.yaml @@ -11,7 +11,7 @@ about: summary: "A python wrapper for libmagic." build: - number: 0 + number: 1 source: url: https://github.com/ahupp/python-magic/archive/{{ version }}.tar.gz @@ -19,10 +19,9 @@ source: sha256: {{ sha256 }} requirements: - build: + host: - python - setuptools - run: - python diff --git a/recipes/rna-seqc/1.1.8/build.sh b/recipes/rna-seqc/1.1.8/build.sh index 827949be..74f26122 100755 --- a/recipes/rna-seqc/1.1.8/build.sh +++ b/recipes/rna-seqc/1.1.8/build.sh @@ -1,6 +1,6 @@ #!/bin/sh -set -e +set -ex mkdir -p "$PREFIX/lib/java/rna-seqc" cp RNA-SeQC.jar "$PREFIX/lib/java/rna-seqc/" diff --git a/recipes/s3cmd/2.0.1-28-gd5e61c3/build.sh b/recipes/s3cmd/2.0.1-28-gd5e61c3/build.sh index e011b675..a58b8225 100644 --- a/recipes/s3cmd/2.0.1-28-gd5e61c3/build.sh +++ b/recipes/s3cmd/2.0.1-28-gd5e61c3/build.sh @@ -1,5 +1,5 @@ #!/bin/sh -set -e +set -ex $PYTHON setup.py install diff --git a/recipes/samtools/1.9+2-g02d93a1/build.sh b/recipes/samtools/1.9+2-g02d93a1/build.sh index 70c84b14..fe272db9 100755 --- a/recipes/samtools/1.9+2-g02d93a1/build.sh +++ b/recipes/samtools/1.9+2-g02d93a1/build.sh @@ -1,8 +1,8 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" autoreconf ./configure --prefix="$PREFIX" \ @@ -10,5 +10,9 @@ autoreconf --without-curses \ CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make -j $n +make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install prefix="$PREFIX" + +mkdir p "$PREFIX/include/samtools" +cp "$SRC_DIR/"*.h "$PREFIX/include/samtools/" +cp "$SRC_DIR/libbam.a" "$PREFIX/lib" diff --git a/recipes/samtools/1.9+2-g02d93a1/meta.yaml b/recipes/samtools/1.9+2-g02d93a1/meta.yaml index e87eacb3..1adca41e 100644 --- a/recipes/samtools/1.9+2-g02d93a1/meta.yaml +++ b/recipes/samtools/1.9+2-g02d93a1/meta.yaml @@ -11,20 +11,46 @@ about: summary: C library for high-throughput sequencing data formats. build: - number: 0 + number: 1 source: git_url: https://github.com/samtools/samtools.git git_rev: 02d93a154a3c27f1acea6021e9e4d75898c2586c -requirements: - build: - - gcc_npg >=7.3 - - htslib =={{ htslib_version }} +outputs: + - name: samtools + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + - make + - perl + host: + - libhts-dev =={{ htslib_version }} + - libz-dev + run: + - libhts + - libz + files: + - bin/ace2sam + - bin/maq2sam-* + - bin/md5* + - bin/plot-bamstats + - bin/samtools + - bin/wgsim + - bin/*.pl + - bin/*.py + test: + commands: + - echo '@HD VN:1.0 SO:coordinate' | samtools view - run: - - htslib =={{ htslib_version }} - -test: - commands: - - echo '@HD VN:1.0 SO:coordinate' | samtools view + - name: samtools-dev + version: {{ version }} + requirements: + run: + - libhts =={{ htslib_version }} + - libz + files: + - include/samtools/*.h + - lib/libbam.a diff --git a/recipes/staden_io_lib/1.14.10/build.sh b/recipes/staden_io_lib/1.14.10/build.sh deleted file mode 100755 index 00268e19..00000000 --- a/recipes/staden_io_lib/1.14.10/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/sh - -set -e - -n=`expr $CPU_COUNT / 4 \| 1` - -./configure --prefix="$PREFIX" --with-zlib="$PREFIX" --with-libcurl="$PREFIX" - -make -j $n -make install prefix="$PREFIX" diff --git a/recipes/staden_io_lib/1.14.10/meta.yaml b/recipes/staden_io_lib/1.14.10/meta.yaml deleted file mode 100644 index feea39aa..00000000 --- a/recipes/staden_io_lib/1.14.10/meta.yaml +++ /dev/null @@ -1,119 +0,0 @@ -{% set version = "1.14.10" %} -{% set sha256 = "c9ef5e3d088148a8bba314aa3b35bba986c161a514dee264939048380120536a" %} - -package: - name: staden_io_lib - version: "{{ version }}" - -about: - home: https://github.com/jkbonfield/io_lib - license: BSD - summary: DNA sequence assembly, editing and analysis tools. - -build: - number: 0 - -source: - url: https://github.com/jkbonfield/io_lib/releases/download/{{ version }}/io_lib-{{ version }}.tar.gz - fn: io_lib-{{ version }}.tar.gz - sha256: {{ sha256 }} - -requirements: - build: - - libbzip2 - - libcurl - - gcc_npg >=7.3 - - liblzma - - zlib - -outputs: - - name: staden_io_lib - version: {{ version }} - requirements: - run: - - libbzip2 - - libcurl - - liblzma - - zlib - files: - - bin/io_lib-config - - lib/libstaden-read* - - include/io_lib - - share/man/man3/ExperimentFile.3 - - share/man/man3/exp2read.3 - - share/man/man3/fread_reading.3 - - share/man/man3/fread_scf.3 - - share/man/man3/fwrite_reading.3 - - share/man/man3/fwrite_scf.3 - - share/man/man3/read2exp.3 - - share/man/man3/read2scf.3 - - share/man/man3/read_allocate.3 - - share/man/man3/read_deallocate.3 - - share/man/man3/read_reading.3 - - share/man/man3/read_scf.3 - - share/man/man3/read_scf_header.3 - - share/man/man3/scf2read.3 - - share/man/man3/write_reading.3 - - share/man/man3/write_scf.3 - - share/man/man3/write_scf_header.3 - - share/man/man4/Read.4 - test: - commands: - - test -f ${PREFIX}/include/io_lib/io_lib_config.h - - test -f ${PREFIX}/lib/libstaden-read.a - - test -h ${PREFIX}/lib/libstaden-read.so - - name: staden_io_bin - version: {{ version }} - requirements: - run: - - staden_io_lib =={{ version }} - - libbzip2 - - libcurl - - liblzma - - zlib - files: - - bin/append_sff - - bin/convert_trace - - bin/cram_dump - - bin/cram_filter - - bin/cram_index - - bin/cram_size - - bin/extract_fastq - - bin/extract_qual - - bin/extract_seq - - bin/get_comment - - bin/hash_exp - - bin/hash_extract - - bin/hash_list - - bin/hash_sff - - bin/hash_tar - - bin/index_tar - - bin/makeSCF - - bin/scf_dump - - bin/scf_info - - bin/scf_update - - bin/scram_flagstat - - bin/scram_merge - - bin/scram_pileup - - bin/scram_test - - bin/scramble - - bin/srf2fasta - - bin/srf2fastq - - bin/srf_dump_all - - bin/srf_extract_hash - - bin/srf_extract_linear - - bin/srf_filter - - bin/srf_index_hash - - bin/srf_info - - bin/srf_list - - bin/trace_dump - - bin/ztr_dump - - share/man/man1/scramble.1 - - share/man/man1/srf2fasta.1 - - share/man/man1/srf2fastq.1 - - share/man/man1/srf_index_hash.1 - - share/man/man1/srf_info.1 - - share/man/man1/srf_list.1 - test: - commands: - - scramble -h diff --git a/recipes/staden_io_lib/1.14.6/meta.yaml b/recipes/staden_io_lib/1.14.6/meta.yaml index 39eaf8ef..dfbcc1c1 100644 --- a/recipes/staden_io_lib/1.14.6/meta.yaml +++ b/recipes/staden_io_lib/1.14.6/meta.yaml @@ -11,66 +11,33 @@ about: summary: DNA sequence assembly, editing and analysis tools. build: - number: 4 + number: 5 source: url: https://sourceforge.net/projects/staden/files/io_lib/{{ version }}/io_lib-{{ version }}.tar.gz/download fn: io_lib-{{ version }}.tar.gz sha256: {{ sha256 }} -requirements: - build: - - libbzip2 - - libcurl - - gcc_npg >=7.3 - - liblzma - - zlib - outputs: - name: staden_io_lib version: {{ version }} requirements: + build: + - {{ compiler("c") }} + - automake + - libtool + - make + host: + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libz-dev run: - - libbzip2 + - {{ pin_subpackage("libstaden-read", exact=True) }} + - libbz2 - libcurl - liblzma - - zlib - files: - - bin/io_lib-config - - lib/libstaden-read* - - include/io_lib - - share/man/man3/ExperimentFile.3 - - share/man/man3/exp2read.3 - - share/man/man3/fread_reading.3 - - share/man/man3/fread_scf.3 - - share/man/man3/fwrite_reading.3 - - share/man/man3/fwrite_scf.3 - - share/man/man3/read2exp.3 - - share/man/man3/read2scf.3 - - share/man/man3/read_allocate.3 - - share/man/man3/read_deallocate.3 - - share/man/man3/read_reading.3 - - share/man/man3/read_scf.3 - - share/man/man3/read_scf_header.3 - - share/man/man3/scf2read.3 - - share/man/man3/write_reading.3 - - share/man/man3/write_scf.3 - - share/man/man3/write_scf_header.3 - - share/man/man4/Read.4 - test: - commands: - - test -f ${PREFIX}/include/io_lib/io_lib_config.h - - test -f ${PREFIX}/lib/libstaden-read.a - - test -h ${PREFIX}/lib/libstaden-read.so - - name: staden_io_bin - version: {{ version }} - requirements: - run: - - staden_io_lib =={{ version }} - - libbzip2 - - libcurl - - liblzma - - zlib + - libz files: - bin/append_sff - bin/convert_trace @@ -117,3 +84,58 @@ outputs: test: commands: - scramble -h + + - name: libstaden-read + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - automake + - libtool + - make + host: + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libz-dev + run: + - libbz2 + - libcurl + - liblzma + - libz + files: + - lib/libstaden-read* + test: + commands: + - test -f ${PREFIX}/lib/libstaden-read.a + - test -h ${PREFIX}/lib/libstaden-read.so + + - name: libstaden-read-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libstaden-read", exact=True) }} + files: + - bin/io_lib-config + - include/io_lib + - share/man/man3/ExperimentFile.3 + - share/man/man3/exp2read.3 + - share/man/man3/fread_reading.3 + - share/man/man3/fread_scf.3 + - share/man/man3/fwrite_reading.3 + - share/man/man3/fwrite_scf.3 + - share/man/man3/read2exp.3 + - share/man/man3/read2scf.3 + - share/man/man3/read_allocate.3 + - share/man/man3/read_deallocate.3 + - share/man/man3/read_reading.3 + - share/man/man3/read_scf.3 + - share/man/man3/read_scf_header.3 + - share/man/man3/scf2read.3 + - share/man/man3/write_reading.3 + - share/man/man3/write_scf.3 + - share/man/man3/write_scf_header.3 + - share/man/man4/Read.4 + test: + commands: + - test -f ${PREFIX}/include/io_lib/io_lib_config.h diff --git a/recipes/staden_io_lib/1.14.9/build.sh b/recipes/staden_io_lib/1.14.9/build.sh index 00268e19..c3d65d2b 100755 --- a/recipes/staden_io_lib/1.14.9/build.sh +++ b/recipes/staden_io_lib/1.14.9/build.sh @@ -1,10 +1,11 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" ./configure --prefix="$PREFIX" --with-zlib="$PREFIX" --with-libcurl="$PREFIX" -make -j $n +make -j $n CPPFLAGS="-I$PREFIX/include" \ + LDFLAGS="-Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib" make install prefix="$PREFIX" diff --git a/recipes/staden_io_lib/1.14.9/meta.yaml b/recipes/staden_io_lib/1.14.9/meta.yaml index ba09fb01..5ac66cde 100644 --- a/recipes/staden_io_lib/1.14.9/meta.yaml +++ b/recipes/staden_io_lib/1.14.9/meta.yaml @@ -11,66 +11,33 @@ about: summary: DNA sequence assembly, editing and analysis tools. build: - number: 4 + number: 5 source: url: https://sourceforge.net/projects/staden/files/io_lib/{{ version }}/io_lib-{{ version }}.tar.gz/download fn: io_lib-{{ version }}.tar.gz sha256: {{ sha256 }} -requirements: - build: - - libbzip2 - - libcurl - - gcc_npg >=7.3 - - liblzma - - zlib - outputs: - name: staden_io_lib version: {{ version }} requirements: + build: + - {{ compiler("c") }} + - automake + - libtool + - make + host: + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libz-dev run: - - libbzip2 + - {{ pin_subpackage("libstaden-read", exact=True) }} + - libbz2 - libcurl - liblzma - - zlib - files: - - bin/io_lib-config - - lib/libstaden-read* - - include/io_lib - - share/man/man3/ExperimentFile.3 - - share/man/man3/exp2read.3 - - share/man/man3/fread_reading.3 - - share/man/man3/fread_scf.3 - - share/man/man3/fwrite_reading.3 - - share/man/man3/fwrite_scf.3 - - share/man/man3/read2exp.3 - - share/man/man3/read2scf.3 - - share/man/man3/read_allocate.3 - - share/man/man3/read_deallocate.3 - - share/man/man3/read_reading.3 - - share/man/man3/read_scf.3 - - share/man/man3/read_scf_header.3 - - share/man/man3/scf2read.3 - - share/man/man3/write_reading.3 - - share/man/man3/write_scf.3 - - share/man/man3/write_scf_header.3 - - share/man/man4/Read.4 - test: - commands: - - test -f ${PREFIX}/include/io_lib/io_lib_config.h - - test -f ${PREFIX}/lib/libstaden-read.a - - test -h ${PREFIX}/lib/libstaden-read.so - - name: staden_io_bin - version: {{ version }} - requirements: - run: - - staden_io_lib =={{ version }} - - libbzip2 - - libcurl - - liblzma - - zlib + - libz files: - bin/append_sff - bin/convert_trace @@ -117,3 +84,58 @@ outputs: test: commands: - scramble -h + + - name: libstaden-read + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - automake + - libtool + - make + host: + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libz-dev + run: + - libbz2 + - libcurl + - liblzma + - libz + files: + - lib/libstaden-read* + test: + commands: + - test -f ${PREFIX}/lib/libstaden-read.a + - test -h ${PREFIX}/lib/libstaden-read.so + + - name: libstaden-read-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libstaden-read", exact=True) }} + files: + - bin/io_lib-config + - include/io_lib + - share/man/man3/ExperimentFile.3 + - share/man/man3/exp2read.3 + - share/man/man3/fread_reading.3 + - share/man/man3/fread_scf.3 + - share/man/man3/fwrite_reading.3 + - share/man/man3/fwrite_scf.3 + - share/man/man3/read2exp.3 + - share/man/man3/read2scf.3 + - share/man/man3/read_allocate.3 + - share/man/man3/read_deallocate.3 + - share/man/man3/read_reading.3 + - share/man/man3/read_scf.3 + - share/man/man3/read_scf_header.3 + - share/man/man3/scf2read.3 + - share/man/man3/write_reading.3 + - share/man/man3/write_scf.3 + - share/man/man3/write_scf_header.3 + - share/man/man4/Read.4 + test: + commands: + - test -f ${PREFIX}/include/io_lib/io_lib_config.h diff --git a/recipes/star/2.5.2b/build.sh b/recipes/star/2.5.2b/build.sh index 8c1bb3cc..c2e2d4a4 100755 --- a/recipes/star/2.5.2b/build.sh +++ b/recipes/star/2.5.2b/build.sh @@ -1,8 +1,8 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" # N.B. CPPFLAGS must reset all the values used by htslib subdirectory, # otherwise they will be lost. Don't set LDFLAGS because the STAR diff --git a/recipes/star/2.5.2b/meta.yaml b/recipes/star/2.5.2b/meta.yaml index cbfb71ef..be69cae4 100644 --- a/recipes/star/2.5.2b/meta.yaml +++ b/recipes/star/2.5.2b/meta.yaml @@ -11,11 +11,7 @@ about: summary: Spliced Transcripts Alignment to a Reference. build: - number: 1 - - rpaths: - - lib64 - - lib + number: 2 source: url: https://github.com/alexdobin/STAR/archive/{{ version }}.tar.gz @@ -24,12 +20,11 @@ source: requirements: build: - - gcc_npg >=7.3 - - zlib - + - {{ compiler("cxx") }} + host: + - libz-dev run: - - libgcc_npg >=7.3 - - zlib + - libz test: commands: diff --git a/recipes/tears/1.2.4/build.sh b/recipes/tears/1.2.4/build.sh index 571d09cb..0ebf96da 100755 --- a/recipes/tears/1.2.4/build.sh +++ b/recipes/tears/1.2.4/build.sh @@ -1,10 +1,12 @@ #!/bin/sh -set -e +set -ex autoreconf -fi -./configure --prefix="$PREFIX" --with-irods="$PREFIX" CPPFLAGS="-I$PREFIX/include -I$PREFIX/include/irods" LDFLAGS="-L$PREFIX/lib -L$PREFIX/lib/irods/externals" +./configure --prefix="$PREFIX" --with-irods="$PREFIX" \ + CPPFLAGS="-I$PREFIX/include -I$PREFIX/include/irods" \ + LDFLAGS="-L$PREFIX/lib -L$PREFIX/lib/irods/externals" -make +make CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install prefix="$PREFIX" diff --git a/recipes/tears/1.2.4/meta.yaml b/recipes/tears/1.2.4/meta.yaml index e8480b0b..f423b707 100644 --- a/recipes/tears/1.2.4/meta.yaml +++ b/recipes/tears/1.2.4/meta.yaml @@ -6,28 +6,30 @@ package: about: home: https://github.com/whitwham/tears - license: GPLv3 + license: GPL3 summary: Stream files to and from iRODS. build: - number: 1 + number: 2 source: git_url: https://github.com/whitwham/tears.git git_rev: v{{ version }} -features: - - irods - requirements: build: - - gcc_npg + - {{ compiler("c") }} + - autoconf + - make + - perl + host: - irods-dev ==4.1.12 - - jansson - + - libjansson-dev + - libssl-dev run: - irods-plugins ==4.1.12 - - jansson + - libjansson + - libssl test: commands: diff --git a/recipes/teepot/1.2.0/build.sh b/recipes/teepot/1.2.0/build.sh index 70017a47..294d1e39 100755 --- a/recipes/teepot/1.2.0/build.sh +++ b/recipes/teepot/1.2.0/build.sh @@ -1,8 +1,8 @@ #!/bin/sh -set -e +set -ex -./configure --prefix="$PREFIX" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib -pthread" +./configure --prefix="$PREFIX" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make +make CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib -lpthread" make install prefix="$PREFIX" diff --git a/recipes/teepot/1.2.0/meta.yaml b/recipes/teepot/1.2.0/meta.yaml index 4706af39..de13e14f 100644 --- a/recipes/teepot/1.2.0/meta.yaml +++ b/recipes/teepot/1.2.0/meta.yaml @@ -11,8 +11,8 @@ about: summary: A spillable pipe buffer. build: - number: 1 - + number: 2 + source: url: https://github.com/wtsi-npg/teepot/releases/download/{{ version }}/teepot-1.2.0.tar.gz fn: teepot-{{ version }}.tar.gz @@ -20,7 +20,8 @@ source: requirements: build: - - gcc_npg >=7.3 + - {{ compiler("c") }} + - make test: commands: diff --git a/recipes/tophat2/2.1.1/build.sh b/recipes/tophat2/2.1.1/build.sh index 45dab8ee..7dde45a9 100755 --- a/recipes/tophat2/2.1.1/build.sh +++ b/recipes/tophat2/2.1.1/build.sh @@ -1,11 +1,15 @@ #!/bin/sh -set -e +set -ex n=1 # Using --with-boost avoids picking up /usr/lib boost, if present. -./configure --prefix="$PREFIX" --with-boost="$PREFIX" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +./configure --prefix="$PREFIX" \ + --with-boost="$PREFIX" \ + CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make -j $n +make -j $n CC="$GCC" \ + INCLUDES="-I. -I$PREFIX/include" LIBPATH="-L$PREFIX/lib" \ + CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install prefix="$PREFIX" diff --git a/recipes/tophat2/2.1.1/conda_build_config.yaml b/recipes/tophat2/2.1.1/conda_build_config.yaml new file mode 100644 index 00000000..15150c0f --- /dev/null +++ b/recipes/tophat2/2.1.1/conda_build_config.yaml @@ -0,0 +1,6 @@ +c_compiler_version: + - 5.4 + +cxx_compiler_version: + - 5.4 + diff --git a/recipes/tophat2/2.1.1/meta.yaml b/recipes/tophat2/2.1.1/meta.yaml index bdb59080..f35f7e6b 100644 --- a/recipes/tophat2/2.1.1/meta.yaml +++ b/recipes/tophat2/2.1.1/meta.yaml @@ -11,7 +11,7 @@ about: summary: Spliced read mapper for RNA-Seq. build: - number: 0 + number: 1 source: url: http://ccb.jhu.edu/software/tophat/downloads/tophat-{{ version }}.tar.gz @@ -20,14 +20,15 @@ source: requirements: build: - - boost - - gcc_npg >=5.5,<7.0.0 - - zlib - + - {{ compiler("c") }} + - {{ compiler("cxx") }} + - make + host: + - libboost-dev + - libz-dev run: - - boost - - libgcc_npg >=5.5 - - zlib + - libboost + - libz test: commands: diff --git a/recipes/verifybamid/1.1.3/build.sh b/recipes/verifybamid/1.1.3/build.sh index 0374bce5..fdf573a9 100755 --- a/recipes/verifybamid/1.1.3/build.sh +++ b/recipes/verifybamid/1.1.3/build.sh @@ -1,15 +1,12 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" -export CPPFLAGS="-I$PREFIX/include" -export LDFLAGS="-L$PREFIX/lib" - -cd libstatgen -make -j $n +cd libStatGen +make -j $n CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" cd ../verifybamid -make -j $n -make install INSTALLDIR="$PREFIX/bin" LIB_PATH_GENERAL="../libstatgen" +make -j $n CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make install INSTALLDIR="$PREFIX/bin" LIB_PATH_GENERAL="../libStatGen" diff --git a/recipes/verifybamid/1.1.3/conda_build_config.yaml b/recipes/verifybamid/1.1.3/conda_build_config.yaml new file mode 100644 index 00000000..54d7f516 --- /dev/null +++ b/recipes/verifybamid/1.1.3/conda_build_config.yaml @@ -0,0 +1,5 @@ +c_compiler_version: + - 5.4 + +cxx_compiler_version: + - 5.4 diff --git a/recipes/verifybamid/1.1.3/libStatGen.patch b/recipes/verifybamid/1.1.3/libStatGen.patch new file mode 100644 index 00000000..11c03235 --- /dev/null +++ b/recipes/verifybamid/1.1.3/libStatGen.patch @@ -0,0 +1,73 @@ +diff --git Makefiles/Makefile.lib Makefiles/Makefile.lib +index f2c653b..097f346 100644 +--- Makefiles/Makefile.lib ++++ Makefiles/Makefile.lib +@@ -34,11 +34,11 @@ profile: $(STAT_GEN_LIB_PROFILE) + # To build the library, build the objects + # Then add them to the library + $(STAT_GEN_LIB_OPT): $(OBJECTS_OPT) +- ar -cru $@ $(OBJECTS_OPT) ++ $(AR) -cru $@ $(OBJECTS_OPT) + $(STAT_GEN_LIB_DEBUG): $(OBJECTS_DEBUG) +- ar -cru $@ $(OBJECTS_DEBUG) ++ $(AR) -cru $@ $(OBJECTS_DEBUG) + $(STAT_GEN_LIB_PROFILE): $(OBJECTS_PROFILE) +- ar -cru $@ $(OBJECTS_PROFILE) ++ $(AR) -cru $@ $(OBJECTS_PROFILE) + + UNAME=$(shell uname) + +diff --git Makefiles/Makefile.src Makefiles/Makefile.src +index 590b468..dc67c47 100644 +--- Makefiles/Makefile.src ++++ Makefiles/Makefile.src +@@ -20,9 +20,9 @@ MAKEFILES_PATH := $(dir $(lastword $(MAKEFILE_LIST))) + include $(MAKEFILES_PATH)Makefile.ext + + # Set the build commands for executable +-OPT_BUILD = $(CXX) $(COMPFLAGS) $(USER_LINK_OPTIONS) -o $(PROG_OPT) $(OBJECTS_OPT) $(USER_LIBS) $(REQ_LIBS_OPT) -lm $(ZLIB_LIB) $(UNAME_LIBS) $(OTHER_LIBS) +-DEBUG_BUILD = $(CXX) $(COMPFLAGS) $(USER_LINK_OPTIONS) -o $(PROG_DEBUG) $(OBJECTS_DEBUG) $(USER_LIBS) $(REQ_LIBS_DEBUG) -lm $(ZLIB_LIB) $(UNAME_LIBS) $(OTHER_LIBS) +-PROFILE_BUILD = $(CXX) $(COMPFLAGS) $(USER_LINK_OPTIONS) -o $(PROG_PROFILE) $(OBJECTS_PROFILE) $(USER_LIBS) $(REQ_LIBS_PROFILE) -lm $(ZLIB_LIB) $(UNAME_LIBS) $(OTHER_LIBS) ++OPT_BUILD = $(CXX) $(COMPFLAGS) $(USER_LINK_OPTIONS) -o $(PROG_OPT) $(OBJECTS_OPT) $(USER_LIBS) $(REQ_LIBS_OPT) $(LDFLAGS) -lm $(ZLIB_LIB) $(UNAME_LIBS) $(OTHER_LIBS) ++DEBUG_BUILD = $(CXX) $(COMPFLAGS) $(USER_LINK_OPTIONS) -o $(PROG_DEBUG) $(OBJECTS_DEBUG) $(USER_LIBS) $(REQ_LIBS_DEBUG) $(LDFLAGS) -lm $(ZLIB_LIB) $(UNAME_LIBS) $(OTHER_LIBS) ++PROFILE_BUILD = $(CXX) $(COMPFLAGS) $(USER_LINK_OPTIONS) -o $(PROG_PROFILE) $(OBJECTS_PROFILE) $(USER_LIBS) $(REQ_LIBS_PROFILE) $(LDFLAGS) -lm $(ZLIB_LIB) $(UNAME_LIBS) $(OTHER_LIBS) + + ADDITIONAL_HELP= @echo "make install Install binaries in $(INSTALLDIR)";\ + echo "make install INSTALLDIR=directory_for_binaries";\ +diff --git Makefiles/Makefile.toolchain Makefiles/Makefile.toolchain +index 36017ed..a82f15b 100644 +--- Makefiles/Makefile.toolchain ++++ Makefiles/Makefile.toolchain +@@ -51,19 +51,19 @@ endif + + # CPP0X=-std=c++0x + +-CXX = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)g++ $(CPP0X) +-CC = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)gcc +-LD = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)ld +-AR = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)ar +-RANLIB = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)ranlib +-OBJCOPY = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)objcopy +-OBJDUMP = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)objdump +-STRIP = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)strip +-NM = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)nm +-SIZE = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)size +-CPP = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)cpp +-AS = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)as +-F77 = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)gfortran ++CXX ?= $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)g++ $(CPP0X) ++CC ?= $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)gcc ++LD ?= $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)ld ++AR ?= $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)ar ++RANLIB ?= $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)ranlib ++OBJCOPY ?= $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)objcopy ++OBJDUMP ?= $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)objdump ++STRIP ?= $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)strip ++NM ?= $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)nm ++SIZE ?= $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)size ++CPP ?= $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)cpp ++AS ?= $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)as ++F77 ?= $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)gfortran + + # + # clang is a drop in replacement for c++ and cc: diff --git a/recipes/verifybamid/1.1.3/meta.yaml b/recipes/verifybamid/1.1.3/meta.yaml index 07f7f924..23e282b1 100644 --- a/recipes/verifybamid/1.1.3/meta.yaml +++ b/recipes/verifybamid/1.1.3/meta.yaml @@ -7,15 +7,11 @@ package: about: home: http://genome.sph.umich.edu - license: Various - summary: Verify identity and purity of sequence data. + license: Other + summary: "Verify identity and purity of sequence data." build: - number: 0 - - rpaths: - - lib64 - - lib + number: 1 source: - git_url: https://github.com/statgen/verifyBamID.git @@ -23,16 +19,21 @@ source: folder: verifybamid - git_url: https://github.com/statgen/libStatGen.git git_rev: v{{ libstatgen_version }} - folder: libstatgen + folder: libStatGen + patches: + - libStatGen.patch requirements: build: - - gcc_npg <7.0 - - zlib - + - {{ compiler("c") }} + - {{ compiler("cxx") }} + - make + host: + - libssl-dev + - libz-dev run: - - libgcc_npg <7.0 - - zlib + - libssl + - libz test: commands: diff --git a/recipes/xz/5.2.3/build.sh b/recipes/xz/5.2.3/build.sh index fce1f273..68c44cfd 100644 --- a/recipes/xz/5.2.3/build.sh +++ b/recipes/xz/5.2.3/build.sh @@ -1,9 +1,9 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" ./configure prefix="$PREFIX" -make -j $n +make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install diff --git a/recipes/xz/5.2.3/meta.yaml b/recipes/xz/5.2.3/meta.yaml index d0e51f8c..f6563524 100644 --- a/recipes/xz/5.2.3/meta.yaml +++ b/recipes/xz/5.2.3/meta.yaml @@ -11,23 +11,22 @@ about: summary: XZ Utils is free general-purpose data compression software. build: - number: 1 + number: 2 source: url: https://tukaani.org/xz/xz-{{ version }}.tar.bz2 fn: xz-{{ version }}.tar.bz2 sha256: {{ sha256 }} -requirements: - build: - - gcc_npg >=7.3 - outputs: - name: xz version: {{ version }} requirements: + build: + - {{ compiler("c") }} + - make run: - - liblzma =={{ version }} + - {{ pin_subpackage('liblzma', exact=True) }} files: - bin/lzless - bin/xzless @@ -59,13 +58,27 @@ outputs: - name: liblzma version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - make files: - - include - - share/doc + - lib/liblzma.* - share/locale - - lib test: commands: - - test -f ${PREFIX}/include/lzma.h - test -f ${PREFIX}/lib/liblzma.a - test -h ${PREFIX}/lib/liblzma.so + + - name: liblzma-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage('liblzma', exact=True) }} + files: + - include + - share/doc + - lib/pkgconfig/liblzma.pc + test: + commands: + - test -f ${PREFIX}/include/lzma.h diff --git a/recipes/zlib/1.2.11/build.sh b/recipes/zlib/1.2.11/build.sh index f7d96bf1..e3885af6 100644 --- a/recipes/zlib/1.2.11/build.sh +++ b/recipes/zlib/1.2.11/build.sh @@ -1,9 +1,9 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" -prefix="$PREFIX" ./configure -make -j $n +prefix="$PREFIX" CC="$GCC" ./configure +make -j $n CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install diff --git a/recipes/zlib/1.2.11/meta.yaml b/recipes/zlib/1.2.11/meta.yaml index 03c218b4..e7e3058b 100644 --- a/recipes/zlib/1.2.11/meta.yaml +++ b/recipes/zlib/1.2.11/meta.yaml @@ -11,8 +11,8 @@ about: summary: A Massively Spiffy Yet Delicately Unobtrusive Compression Library. build: - number: 0 - + number: 1 + source: url: https://sourceforge.mirrorservice.org/l/li/libpng/zlib/{{ version }}/zlib-{{ version }}.tar.gz fn: zlib-{{ version }}.tar.gz @@ -20,10 +20,32 @@ source: requirements: build: - - gcc_npg >=7.3 + - {{ compiler("c") }} + run: + - {{ pin_subpackage('libz-dev', exact=True) }} + +outputs: + - name: libz + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - make + files: + - lib/libz.* + test: + commands: + - test -f ${PREFIX}/lib/libz.a + - test -h ${PREFIX}/lib/libz.so -test: - commands: - - test -f ${PREFIX}/include/zlib.h - - test -f ${PREFIX}/lib/libz.a - - test -h ${PREFIX}/lib/libz.so + - name: libz-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage('libz', exact=True) }} + files: + - include + - lib/pkgconfig/zlib.pc + test: + commands: + - test -f ${PREFIX}/include/zlib.h From fe01fc1462f6a130d2509e77287a6bde4705ce53 Mon Sep 17 00:00:00 2001 From: Keith James Date: Wed, 12 Dec 2018 16:17:07 +0000 Subject: [PATCH 003/119] Added a package sorting script to determine from-source build order from the recipes. --- scripts/package_sort.py | 353 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 353 insertions(+) create mode 100755 scripts/package_sort.py diff --git a/scripts/package_sort.py b/scripts/package_sort.py new file mode 100755 index 00000000..4292704a --- /dev/null +++ b/scripts/package_sort.py @@ -0,0 +1,353 @@ +#!/usr/bin/env python3 +# +# Copyright © 2018 Genome Research Ltd. All rights reserved. +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +# +# @author Keith James + +from packaging.version import Version, LegacyVersion, parse +from packaging.specifiers import SpecifierSet + +import jinja2 as jj +import logging as log +import networkx as nx + +import argparse +import functools +import os +import sys +import yaml + + +def parse_requirement(req_str): + """ + Parse a software version requirement string conforming to the Conda + match specification (Note: the OR operator '|' is not supported + currently). + + e.g gcc >=4.6,<7.0 + + The PEP440 package name and version specifier returned may be used + to identify software that will fulfill the requirement described + by the argument. + + :param req_str str: The requirement Conda match specification. + + :returns: The required package name, a combined required version + specifier. + + :rtype: str, packaging.specifiers.SpecifierSet + """ + parts = list(map(str.strip, req_str.split())) + pkg_name = parts[0] + spec_set = None + + if len(parts) > 1: + spec_strs = parts[1].split(',') + specs = [SpecifierSet(x) for x in spec_strs] + spec_set = functools.reduce(lambda vx, vy: vx & vy, specs) + + return pkg_name, spec_set + + +def find_recipe_files(dir): + """ + Return the absolute paths of Conda recipe meta.yaml files in a + directory, recursively. + + :param dir str: The directory to search. + + :returns: Paths of recipe files. + + :rtype: list str + """ + recipe_files = [] + for dir, _, files in os.walk(base): + for file in files: + if file == 'meta.yaml': + recipe_files.append(os.path.join(dir, file)) + return recipe_files + + +def make_template_env(recipe_files): + """ + Make a new Jinjer2 template environment by loading Conda recipes + as templates. Add some dummy template expansion functions so that + we don't need the Conda itself to process the recipes. + + :param recipe_files list str: Paths of recipe files. + + :returns: A Jinja2 Environment + + :rtype: jinja2.Environment + """ + templates = {} + for f in recipe_files: + with open(f) as t: + templates[f] = t.read() + + # Hack to expand templates. The value of this may safely be incorrect; + # we don't use the value, we simply need a dummy value to permit + # template expansion. + template_loader = jj.DictLoader(templates) + template_env = jj.Environment(loader=template_loader) + template_env.globals['PKG_BUILDNUM'] = 9999 + template_env.globals['compiler'] = lambda *args, **kwargs: None + + # Don't declare sub-package dependecies because they refer to + # their own package and introduce a cycle in the graph. + template_env.globals['pin_subpackage'] = lambda *args, **kwargs: None + return template_env + + +def render_recipe(recipe_file, template_env): + """ + Render a Conda recipe file (which contains Jinja2 templates) into + a valid YAML document so that we can parse it. Return the YAML + document. + + :param recipe_file str: The recipe file path. + + :param template_env jinja2.Environment: The Jinja2 template + environment to use. + + :returns: YAML document. + + :rtype: str + """ + log.info("Working on %s", recipe_file) + template = template_env.get_template(recipe_file) + return template.render() + + +def find_package_version(req_pkg, pkg_index, spec=None): + """ + Return any available versions of a package within a range, or all + versions if no range limit is supplied. + + :param req_pkg str: A package name. + + :param pkg_index dict: A mapping of package name to liost of + availble versions. + + :param spec packaging.specifiers.Specifier: A specifier for + acceptable versions. + + :returns: A list of matching versions. + + :rtype: list + """ + candidates = pkg_index[req_pkg] + return list(spec.filter(candidates)) if spec else candidates + + +def load_recipes(dir): + recipe_files = find_recipe_files(base) + template_env = make_template_env(recipe_files) + + # Append to a dict list value + def add_listval(dikt, key, value): + if key in dikt: + dikt[key].append(value) + else: + dikt[key] = [value] + + # This dict contains lists of Versions of package. + # + # Key: package name + # + # Value: list of Versions of the package + pkg_versions = {} + + # This dict describes the dependencies of a specific package + # Version. Dependencies may change from one version of a package + # to another. + # + # Key: (package name, Version) tuple + # + # Value: list of (package name, version Specifier) tuples of dependencies + pkg_requirements = {} + + # This dict describes the sub-packages produced by a package. + # + # Key: sub-package name + # + # Value: parent package name + # + pkg_outputs = {} + + for recipe_file in recipe_files: + log.debug("recipe_file: %s", recipe_file) + recipe = yaml.safe_load(render_recipe(recipe_file, template_env)) + + pkg = recipe["package"] + pkg_name = pkg["name"] + + pkg_version = parse(pkg["version"]) + add_listval(pkg_versions, pkg_name, pkg_version) + log.debug("package name: %s %s", pkg_name, pkg_version) + + pkg_reqs = [] + base_reqs = recipe.get("requirements", {}) + pkg_reqs += base_reqs.get("host", []) + pkg_reqs += base_reqs.get("run", []) + + # Also search outputs for requirements + outputs = recipe.get("outputs", []) + for output in outputs: + output_name = output["name"] + pkg_outputs[output_name] = pkg_name + + output_reqs = output.get("requirements", {}) + pkg_reqs += output_reqs.get("host", []) + pkg_reqs += output_reqs.get("run", []) + + for pkg_req in pkg_reqs: + req, spec = parse_requirement(pkg_req) + if req is not 'None': + log.debug("%s version: %s requires %s version: %s", + pkg_name, pkg_version, req, spec) + add_listval(pkg_requirements, (pkg_name, pkg_version), + (req, spec)) + + return pkg_versions, pkg_requirements, pkg_outputs + + +def build_dependency_graph(graph, root_node, + pkg_versions, pkg_reqs, pkg_outputs): + """ + Return a dependency DAG built from the data extracted from recipes + by the load_recipes function. + """ + graph.add_node(root_node) + + for pkg_name, versions in pkg_versions.items(): + for version in versions: + ptup = (pkg_name, version) + if ptup in pkg_reqs: + reqs = pkg_reqs[ptup] + log.debug("%s requires %s", ptup, reqs) + + for (req_pkg, spec) in reqs: + # Is the required package one of the packages we + # are building? + if req_pkg in pkg_versions: + v = max(find_package_version(req_pkg, + pkg_versions, + spec=spec)) + rtup = (req_pkg, v) + graph.add_edge(rtup, ptup) + + log.debug("Need to build package " + "%s %s of candidates %s", + req_pkg, v, pkg_versions[req_pkg]) + # Is the required package one of the sub-packages + # of the packages we are building? + else: + if req_pkg in pkg_outputs: + # Require the parent package rather than + # the sub-package + parent_pkg = pkg_outputs[req_pkg] + v = max(find_package_version(parent_pkg, + pkg_versions, + spec=spec)) + rtup = (parent_pkg, v) + graph.add_edge(rtup, ptup) + + log.debug("Need to build (containing) package " + "%s %s of candidates %s", + parent_pkg, v, pkg_versions[parent_pkg]) + else: + log.warn("Can't find required package %s", req_pkg) + else: + log.debug("%s has no requirements", ptup) + graph.add_edge(ptup, root_node) + return graph + + + +description = """ +Reads Conda package recipe meta.yaml files under the specified +directory (recursively) and reports package dependency information. + +If no package is specified, a directed, acyclic graph of the +inter-package dependencies is calculated, and a topological sort of +that graph is printed to STDOUT. The utility of this is that it +describes an order in which to build packages whereby a later package +will only depend on previously built packages, never on package yet to +be built. This feature is essential because conda-build is no longer +capable of recursive from-source builds [1]. + +If a package and version are specified, a directed, acyclic graph of +the inter-package dependencies of its ancestors is calculated, and a +topological sort of that graph is printed to STDOUT. This describes +the sub-graph of packages that must be built prior to the specified +package version. + +1. https://github.com/conda/conda-build/issues/2467 + +""" + + +parser = argparse.ArgumentParser(description=description) + +parser.add_argument("recipes", + help="Recipes directory, defaults to current directory", + type=str, nargs="?", default=".") + +parser.add_argument("-p", "--package", type=str, + help="Report dependentss (i.e. descendants) of the" + "specified package") +parser.add_argument("-v", "--version", type=str, + help="Report dependents (i.e. descendants) of the" + "specified package version") + +parser.add_argument("--debug", + help="Enable DEBUG level logging to STDERR", + action="store_true") +parser.add_argument("--verbose", + help="Enable INFO level logging to STDERR", + action="store_true") + +args = parser.parse_args() + +level = log.ERROR +if args.debug: + level = log.DEBUG +elif args.verbose: + level = log.INFO +log.basicConfig(level=level) + +base = args.recipes + +pkg_versions, pkg_requirements, pkg_outputs = load_recipes(base) + +root_node="root" +graph = nx.DiGraph(directed=True) +graph = build_dependency_graph(graph, root_node, + pkg_versions, pkg_requirements, pkg_outputs) +if args.package and args.version: + pv = (args.package, parse(args.version)) + if pv in graph: + for node in nx.topological_sort( + nx.subgraph(graph, nx.ancestors(graph, pv))): + print(node[0], node[1]) + else: + raise ValueError("Package {} version {} is not present " + "in the graph".format(pv[0], pv[1])) +else: + for node in nx.topological_sort(graph): + if node is not root_node: + print(node[0], node[1]) From a98bdde93950d080eeb33b3c1cb0c908683871bc Mon Sep 17 00:00:00 2001 From: Keith James Date: Thu, 13 Dec 2018 09:26:41 +0000 Subject: [PATCH 004/119] Removed old recipes. --- recipes/bambi/0.10.1/build.sh | 12 -- recipes/bambi/0.10.1/meta.yaml | 33 ---- recipes/bambi/0.11.0/build.sh | 12 -- recipes/bambi/0.11.0/meta.yaml | 33 ---- recipes/baton/1.0.1/build.sh | 10 -- recipes/baton/1.0.1/meta.yaml | 36 ----- recipes/bcftools/1.6/build.sh | 10 -- recipes/bcftools/1.6/meta.yaml | 27 ---- recipes/bcftools/1.7/build.sh | 10 -- recipes/bcftools/1.7/meta.yaml | 27 ---- recipes/bcftools/1.8/build.sh | 10 -- recipes/bcftools/1.8/meta.yaml | 27 ---- recipes/boost/1.47.0/build.sh | 9 -- recipes/boost/1.47.0/meta.yaml | 43 ------ recipes/bwa/0.5.10-mt_fixes.2/Makefile.patch | 19 --- recipes/bwa/0.5.10-mt_fixes.2/build.sh | 15 -- recipes/bwa/0.5.10-mt_fixes.2/meta.yaml | 30 ---- recipes/cmake/2.8.9/build.sh | 11 -- recipes/cmake/2.8.9/meta.yaml | 35 ----- recipes/cmake/3.10.2/build.sh | 11 -- recipes/cmake/3.10.2/meta.yaml | 35 ----- recipes/gcc_npg/4.6.4/build.sh | 50 ------- recipes/gcc_npg/4.6.4/meta.yaml | 72 --------- recipes/gcc_npg/5.5.0/build.sh | 58 ------- recipes/gcc_npg/5.5.0/meta.yaml | 80 ---------- recipes/gcc_npg/7.3.0/build.sh | 58 ------- recipes/gcc_npg/7.3.0/meta.yaml | 80 ---------- recipes/hdf5/1.8.20/build.sh | 10 -- recipes/hdf5/1.8.20/meta.yaml | 70 --------- recipes/htslib/1.5/build.sh | 12 -- recipes/htslib/1.5/meta.yaml | 79 ---------- recipes/htslib/1.6/build.sh | 12 -- recipes/htslib/1.6/meta.yaml | 80 ---------- recipes/htslib/1.7/build.sh | 12 -- recipes/htslib/1.7/meta.yaml | 80 ---------- recipes/htslib/1.8+25-gc167fee/README.md | 3 - recipes/htslib/1.8+25-gc167fee/build.sh | 20 --- recipes/htslib/1.8+25-gc167fee/meta.yaml | 80 ---------- recipes/htslib/1.8+48-g6cd9f24/README.md | 3 - recipes/htslib/1.8+48-g6cd9f24/build.sh | 20 --- recipes/htslib/1.8+48-g6cd9f24/meta.yaml | 80 ---------- recipes/htslib/1.8/build.sh | 16 -- recipes/htslib/1.8/meta.yaml | 80 ---------- recipes/minimap2/2.8/Makefile.patch | 15 -- recipes/minimap2/2.8/build.sh | 13 -- recipes/minimap2/2.8/meta.yaml | 33 ---- recipes/nanopolish/0.8.5/build.sh | 12 -- recipes/nanopolish/0.8.5/meta.yaml | 41 ----- .../patch-build-system-htslib-gomp.patch | 53 ------- recipes/nodejs/6.12.2/build.sh | 10 -- recipes/nodejs/6.12.2/meta.yaml | 38 ----- recipes/porechop/0.2.3/build.sh | 5 - recipes/porechop/0.2.3/meta.yaml | 35 ----- recipes/samtools/1.5/build.sh | 10 -- recipes/samtools/1.5/meta.yaml | 31 ---- recipes/samtools/1.6/build.sh | 10 -- recipes/samtools/1.6/meta.yaml | 31 ---- recipes/samtools/1.7/build.sh | 10 -- recipes/samtools/1.7/meta.yaml | 31 ---- recipes/samtools/1.8+27-g0896262/README.md | 2 - recipes/samtools/1.8+27-g0896262/build.sh | 14 -- recipes/samtools/1.8+27-g0896262/meta.yaml | 30 ---- recipes/samtools/1.8+59-g4da22a9/README.md | 2 - recipes/samtools/1.8+59-g4da22a9/build.sh | 14 -- recipes/samtools/1.8+59-g4da22a9/meta.yaml | 30 ---- recipes/samtools/1.8/build.sh | 13 -- recipes/samtools/1.8/meta.yaml | 31 ---- recipes/staden_io_lib/1.14.6/build.sh | 10 -- recipes/staden_io_lib/1.14.6/meta.yaml | 141 ------------------ recipes/staden_io_lib/1.14.9/build.sh | 11 -- recipes/staden_io_lib/1.14.9/meta.yaml | 141 ------------------ recipes/tears/1.2.3/build.sh | 10 -- recipes/tears/1.2.3/meta.yaml | 35 ----- recipes/tophat2/2.0.14/build.sh | 11 -- recipes/tophat2/2.0.14/meta.yaml | 34 ----- recipes/util-linux/2.32/build.sh | 75 ---------- recipes/util-linux/2.32/meta.yaml | 49 ------ recipes/wr/0.11.0/build.sh | 12 -- recipes/wr/0.11.0/meta.yaml | 24 --- recipes/wr/0.12.0/build.sh | 12 -- recipes/wr/0.12.0/meta.yaml | 24 --- recipes/wr/0.13.0/build.sh | 12 -- recipes/wr/0.13.0/meta.yaml | 24 --- recipes/wr/0.14.0/build.sh | 12 -- recipes/wr/0.14.0/meta.yaml | 24 --- recipes/wr/0.15.0/build.sh | 12 -- recipes/wr/0.15.0/meta.yaml | 24 --- 87 files changed, 2721 deletions(-) delete mode 100755 recipes/bambi/0.10.1/build.sh delete mode 100644 recipes/bambi/0.10.1/meta.yaml delete mode 100755 recipes/bambi/0.11.0/build.sh delete mode 100644 recipes/bambi/0.11.0/meta.yaml delete mode 100755 recipes/baton/1.0.1/build.sh delete mode 100644 recipes/baton/1.0.1/meta.yaml delete mode 100755 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100644 recipes/wr/0.13.0/build.sh delete mode 100644 recipes/wr/0.13.0/meta.yaml delete mode 100644 recipes/wr/0.14.0/build.sh delete mode 100644 recipes/wr/0.14.0/meta.yaml delete mode 100644 recipes/wr/0.15.0/build.sh delete mode 100644 recipes/wr/0.15.0/meta.yaml diff --git a/recipes/bambi/0.10.1/build.sh b/recipes/bambi/0.10.1/build.sh deleted file mode 100755 index 1a1c597a..00000000 --- a/recipes/bambi/0.10.1/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/bin/sh - -set -e - -autoreconf -fi - -n=`expr $CPU_COUNT / 4 \| 1` - -./configure --prefix="$PREFIX" --with-htslib="$PREFIX" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" - -make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make install prefix="$PREFIX" diff --git a/recipes/bambi/0.10.1/meta.yaml b/recipes/bambi/0.10.1/meta.yaml deleted file mode 100644 index 01e4c766..00000000 --- a/recipes/bambi/0.10.1/meta.yaml +++ /dev/null @@ -1,33 +0,0 @@ -{% set version = "0.10.1" %} - -package: - name: bambi - version: "{{ version }}" - -about: - home: https://github.com/wtsi-npg/bambi - license: AGPL - summary: A set of programs to manipulate SAM/BAM/CRAM files, using HTSLIB. - -build: - number: 0 - -source: - git_url: https://github.com/wtsi-npg/bambi.git - git_rev: 0.10.1 - -requirements: - build: - - gcc_npg >=7.3 - - htslib >=1.7 - - libgd - - libxml2 - - run: - - htslib >=1.7 - - libgd - - libxml2 - -test: - commands: - - bambi --version diff --git a/recipes/bambi/0.11.0/build.sh b/recipes/bambi/0.11.0/build.sh deleted file mode 100755 index 1a1c597a..00000000 --- a/recipes/bambi/0.11.0/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/bin/sh - -set -e - -autoreconf -fi - -n=`expr $CPU_COUNT / 4 \| 1` - -./configure --prefix="$PREFIX" --with-htslib="$PREFIX" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" - -make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make install prefix="$PREFIX" diff --git a/recipes/bambi/0.11.0/meta.yaml b/recipes/bambi/0.11.0/meta.yaml deleted file mode 100644 index afbd0920..00000000 --- a/recipes/bambi/0.11.0/meta.yaml +++ /dev/null @@ -1,33 +0,0 @@ -{% set version = "0.11.0" %} - -package: - name: bambi - version: "{{ version }}" - -about: - home: https://github.com/wtsi-npg/bambi - license: AGPL - summary: A set of programs to manipulate SAM/BAM/CRAM files, using HTSLIB. - -build: - number: 0 - -source: - git_url: https://github.com/wtsi-npg/bambi.git - git_rev: 0.11.0 - -requirements: - build: - - gcc_npg >=7.3 - - htslib >=1.8 - - libgd - - libxml2 - - run: - - htslib >=1.8 - - libgd - - libxml2 - -test: - commands: - - bambi --version diff --git a/recipes/baton/1.0.1/build.sh b/recipes/baton/1.0.1/build.sh deleted file mode 100755 index 593faefb..00000000 --- a/recipes/baton/1.0.1/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/sh - -set -e - -n=`expr $CPU_COUNT / 4 \| 1` - -./configure --prefix="$PREFIX" --with-irods="$PREFIX" CPPFLAGS="-I$PREFIX/include/irods" LDFLAGS="-L$PREFIX/lib -L$PREFIX/lib/irods/externals" - -make -j $n -make install prefix="$PREFIX" diff --git a/recipes/baton/1.0.1/meta.yaml b/recipes/baton/1.0.1/meta.yaml deleted file mode 100644 index 25fff8fa..00000000 --- a/recipes/baton/1.0.1/meta.yaml +++ /dev/null @@ -1,36 +0,0 @@ -{% set version = "1.0.1" %} -{% set sha256 = "db34f008e3f775b8a72f01a3bf8cca70c81d8f927992424395585b7f9b23f2a8" %} - -package: - name: baton - version: "{{ version }}" - -about: - home: https://github.com/wtsi-npg/baton - license: GPL2 - summary: Client programs and API for use with iRODS (Integrated Rule-Oriented Data System). - -build: - number: 0 - -source: - url: https://github.com/wtsi-npg/baton/releases/download/{{ version }}/baton-{{ version }}.tar.gz - fn: baton-{{ version }}.tar.gz - sha256: {{ sha256 }} - -features: - - irods - -requirements: - build: - - gcc_npg >=7.3 - - irods-dev - - jansson - - run: - - jansson - - libgcc_npg >=7.3 - -test: - commands: - - baton-list --version diff --git a/recipes/bcftools/1.6/build.sh b/recipes/bcftools/1.6/build.sh deleted file mode 100755 index 69ce52be..00000000 --- a/recipes/bcftools/1.6/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/sh - -set -e - -n=`expr $CPU_COUNT / 4 \| 1` - -./configure --prefix="$PREFIX" --with-htslib="$PREFIX" - -make -j $n # Workaround https://github.com/samtools/bcftools/issues/727 -make install prefix="$PREFIX" diff --git a/recipes/bcftools/1.6/meta.yaml b/recipes/bcftools/1.6/meta.yaml deleted file mode 100644 index 9188ec99..00000000 --- a/recipes/bcftools/1.6/meta.yaml +++ /dev/null @@ -1,27 +0,0 @@ -{% set version = "1.6" %} -{% set sha256 = "293010736b076cf684d2873928924fcc3d2c231a091084c2ac23a8045c7df982" %} - -package: - name: bcftools - version: "{{ version }}" - -about: - home: https://github.com/samtools/samtools - license: MIT - summary: C library for high-throughput sequencing data formats. - -build: - number: 0 - -source: - url: https://github.com/samtools/bcftools/releases/download/{{ version }}/bcftools-{{ version }}.tar.bz2 - fn: bcftools-{{ version }}.tar.bz2 - sha256: {{ sha256 }} - -requirements: - build: - - gcc_npg >=7.3 - - htslib =={{ version }} - - run: - - htslib =={{ version }} diff --git a/recipes/bcftools/1.7/build.sh b/recipes/bcftools/1.7/build.sh deleted file mode 100755 index caf5544c..00000000 --- a/recipes/bcftools/1.7/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/sh - -set -e - -n=`expr $CPU_COUNT / 4 \| 1` - -./configure --prefix="$PREFIX" --with-htslib="$PREFIX" - -make -j $n -make install prefix="$PREFIX" diff --git a/recipes/bcftools/1.7/meta.yaml b/recipes/bcftools/1.7/meta.yaml deleted file mode 100644 index b97bc06d..00000000 --- a/recipes/bcftools/1.7/meta.yaml +++ /dev/null @@ -1,27 +0,0 @@ -{% set version = "1.7" %} -{% set sha256 = "dd4f63d91b0dffb0f0ce88ac75c2387251930c8063f7799611265083f8d302d1" %} - -package: - name: bcftools - version: "{{ version }}" - -about: - home: https://github.com/samtools/samtools - license: MIT - summary: C library for high-throughput sequencing data formats. - -build: - number: 0 - -source: - url: https://github.com/samtools/bcftools/releases/download/{{ version }}/bcftools-{{ version }}.tar.bz2 - fn: bcftools-{{ version }}.tar.bz2 - sha256: {{ sha256 }} - -requirements: - build: - - gcc_npg >=7.3 - - htslib =={{ version }} - - run: - - htslib =={{ version }} diff --git a/recipes/bcftools/1.8/build.sh b/recipes/bcftools/1.8/build.sh deleted file mode 100755 index caf5544c..00000000 --- a/recipes/bcftools/1.8/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/sh - -set -e - -n=`expr $CPU_COUNT / 4 \| 1` - -./configure --prefix="$PREFIX" --with-htslib="$PREFIX" - -make -j $n -make install prefix="$PREFIX" diff --git a/recipes/bcftools/1.8/meta.yaml b/recipes/bcftools/1.8/meta.yaml deleted file mode 100644 index 49753228..00000000 --- a/recipes/bcftools/1.8/meta.yaml +++ /dev/null @@ -1,27 +0,0 @@ -{% set version = "1.8" %} -{% set sha256 = "4acbfd691f137742e0be63d09f516434f0faf617a5c60f466140e0677915fced" %} - -package: - name: bcftools - version: "{{ version }}" - -about: - home: https://github.com/samtools/samtools - license: MIT - summary: C library for high-throughput sequencing data formats. - -build: - number: 0 - -source: - url: https://github.com/samtools/bcftools/releases/download/{{ version }}/bcftools-{{ version }}.tar.bz2 - fn: bcftools-{{ version }}.tar.bz2 - sha256: {{ sha256 }} - -requirements: - build: - - gcc_npg >=7.3 - - htslib =={{ version }} - - run: - - htslib =={{ version }} diff --git a/recipes/boost/1.47.0/build.sh b/recipes/boost/1.47.0/build.sh deleted file mode 100644 index c1d09eb1..00000000 --- a/recipes/boost/1.47.0/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/sh - -set -e - -n=$CPU_COUNT - -./bootstrap.sh --prefix="$PREFIX" - -./b2 -j $n --prefix="$PREFIX" --without-mpi install diff --git a/recipes/boost/1.47.0/meta.yaml b/recipes/boost/1.47.0/meta.yaml deleted file mode 100644 index dfcd70aa..00000000 --- a/recipes/boost/1.47.0/meta.yaml +++ /dev/null @@ -1,43 +0,0 @@ -{% set version = "1.47.0" %} -{% set alt_version = "1_47_0" %} -{% set sha256 = "815a5d9faac4dbd523fbcf3fe1065e443c0bbf43427c44aa423422c6ec4c2e31" %} - -package: - name: boost - version: "{{ version }}" - -about: - home: http://www.boost.org - license: Boost - summary: "Free peer-reviewed portable C++ source libraries." - -build: - number: 2 - - rpaths: - - lib64 - - lib - -source: - url: https://sourceforge.net/projects/boost/files/boost/{{ version }}/boost_{{ alt_version }}.tar.bz2/download - fn: boost_{{ alt_version }}.tar.bz2 - sha256: {{ sha256 }} - -requirements: - build: - - libbzip2 - - gcc_npg >=4.6,<5.0 - - liblzma - - zlib - - run: - - libbzip2 - - libgcc_npg >=4.6,<5.0 - - liblzma - - zlib - -test: - commands: - - test -f ${PREFIX}/include/boost/config.hpp - - test -f ${PREFIX}/lib/libboost_system.a - - test -h ${PREFIX}/lib/libboost_system.so diff --git a/recipes/bwa/0.5.10-mt_fixes.2/Makefile.patch b/recipes/bwa/0.5.10-mt_fixes.2/Makefile.patch deleted file mode 100644 index 76b607f8..00000000 --- a/recipes/bwa/0.5.10-mt_fixes.2/Makefile.patch +++ /dev/null @@ -1,19 +0,0 @@ -*** Makefile 2018-09-19 11:30:16.323723930 +0000 ---- Makefile.1 2018-09-19 11:29:44.126713296 +0000 -*************** -*** 41,47 **** - - bwa:bwt_gen/libbwtgen.a $(OBJS) main.c main.h - d=`date`;\ -! $(CC) $(CFLAGS) -DBLDDATE="$$d" -c main.c -o main.o ;\ - $(CC) $(CFLAGS) $(DFLAGS) $(OBJS) main.o -o $@ $(LIBS) - - depend: ---- 41,47 ---- - - bwa:bwt_gen/libbwtgen.a $(OBJS) main.c main.h - d=`date`;\ -! $(CC) $(CFLAGS) -DBLDDATE="$$d" $(INCLUDES) -c main.c -o main.o ;\ - $(CC) $(CFLAGS) $(DFLAGS) $(OBJS) main.o -o $@ $(LIBS) - - depend: diff --git a/recipes/bwa/0.5.10-mt_fixes.2/build.sh b/recipes/bwa/0.5.10-mt_fixes.2/build.sh deleted file mode 100755 index 734232d5..00000000 --- a/recipes/bwa/0.5.10-mt_fixes.2/build.sh +++ /dev/null @@ -1,15 +0,0 @@ -#!/bin/sh - -set -e - -n=`expr $CPU_COUNT / 4 \| 1` - -make -j $n CFLAGS="-g -Wall -O2 --std=gnu89" \ - INCLUDES="-I. -I.. -I$PREFIX/include" \ - LIBS="-L$PREFIX/lib -lm -lz -lpthread -Lbwt_gen -lbwtgen" - -mkdir -p "$PREFIX/bin" -cp bwa "$PREFIX/bin/" - -mkdir -p "$PREFIX/share/man/man1" -cp bwa.1 "$PREFIX/share/man/man1/" diff --git a/recipes/bwa/0.5.10-mt_fixes.2/meta.yaml b/recipes/bwa/0.5.10-mt_fixes.2/meta.yaml deleted file mode 100644 index 56d3d232..00000000 --- a/recipes/bwa/0.5.10-mt_fixes.2/meta.yaml +++ /dev/null @@ -1,30 +0,0 @@ -{% set version = "0.5.10_mt_fixes.2" %} - -package: - name: bwa-aligner - version: "{{ version }}" - -about: - home: https://github.com/lh3/bwa - license: GPLv3 - summary: Burrows-Wheeler Aligner for short-read alignment. - -build: - number: 0 - -source: - - git_url: https://github.com/wtsi-npg/bwa.git - git_rev: b8267d812d44036f5858baf3353fa5f4ceca06f8 - patches: - - Makefile.patch - -requirements: - build: - - zlib - - run: - - zlib - -test: - commands: - - test -x ${PREFIX}/bin/bwa diff --git a/recipes/cmake/2.8.9/build.sh b/recipes/cmake/2.8.9/build.sh deleted file mode 100755 index c6e55749..00000000 --- a/recipes/cmake/2.8.9/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/sh - -set -e - -n=$CPU_COUNT - -export LD_LIBRARY_PATH="$PREFIX/lib64:$LD_LIBRARY_PATH" -./bootstrap --prefix="$PREFIX" --parallel=$n - -make -j $n -make install prefix="$PREFIX" diff --git a/recipes/cmake/2.8.9/meta.yaml b/recipes/cmake/2.8.9/meta.yaml deleted file mode 100644 index 3c7e02be..00000000 --- a/recipes/cmake/2.8.9/meta.yaml +++ /dev/null @@ -1,35 +0,0 @@ -{% set version = "2.8.9" %} -{% set short_version = "2.8" %} -{% set sha256 = "dc3dcc7399be8636471975f955086cdf800739862c240858a98e89719e45e6f9" %} - -package: - name: cmake - version: "{{ version }}" - -about: - home: https://cmake.org/ - license: CMake - summary: Cross Platform Makefile Generator. - -source: - url: https://cmake.org/files/v{{ short_version }}/cmake-{{ version }}.tar.gz - fn: cmake-{{ version }}.tar.gz - sha256: {{ sha256 }} - -build: - number: 0 - - rpaths: - - lib64 - - lib - -requirements: - build: - - gcc_npg >=7.3 - - run: - - libgcc_npg - -test: - commands: - - cmake --help diff --git a/recipes/cmake/3.10.2/build.sh b/recipes/cmake/3.10.2/build.sh deleted file mode 100755 index c6e55749..00000000 --- a/recipes/cmake/3.10.2/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/sh - -set -e - -n=$CPU_COUNT - -export LD_LIBRARY_PATH="$PREFIX/lib64:$LD_LIBRARY_PATH" -./bootstrap --prefix="$PREFIX" --parallel=$n - -make -j $n -make install prefix="$PREFIX" diff --git a/recipes/cmake/3.10.2/meta.yaml b/recipes/cmake/3.10.2/meta.yaml deleted file mode 100644 index 24759196..00000000 --- a/recipes/cmake/3.10.2/meta.yaml +++ /dev/null @@ -1,35 +0,0 @@ -{% set version = "3.10.2" %} -{% set short_version = "3.10" %} -{% set sha256 = "80d0faad4ab56de07aa21a7fc692c88c4ce6156d42b0579c6962004a70a3218b" %} - -package: - name: cmake - version: "{{ version }}" - -about: - home: https://cmake.org/ - license: CMake - summary: Cross Platform Makefile Generator. - -source: - url: https://cmake.org/files/v{{ short_version }}/cmake-{{ version }}.tar.gz - fn: cmake-{{ version }}.tar.gz - sha256: {{ sha256 }} - -build: - number: 0 - - rpaths: - - lib64 - - lib - -requirements: - build: - - gcc_npg >=7.3 - - run: - - libgcc_npg - -test: - commands: - - cmake --help diff --git a/recipes/gcc_npg/4.6.4/build.sh b/recipes/gcc_npg/4.6.4/build.sh deleted file mode 100755 index 0112456f..00000000 --- a/recipes/gcc_npg/4.6.4/build.sh +++ /dev/null @@ -1,50 +0,0 @@ -#!/bin/sh - -set -e - -n=$CPU_COUNT - - -for pkg in gmp mpfr mpc gcc; do - mkdir -p "$SRC_DIR/$pkg-build" -done - -pushd gmp-src -./configure --disable-shared --enable-static \ - --prefix="$SRC_DIR/gmp-build" \ - CFLAGS="-O2 -pedantic -fomit-frame-pointer -m64 -march=x86-64" \ - MPN_PATH="x86_64 generic" - -make -j $n && make check && make install -popd - -pushd mpfr-src -./configure --disable-shared --enable-static \ - --prefix="$SRC_DIR/mpfr-build" \ - --with-gmp="$SRC_DIR/gmp-build" - -make -j $n && make check && make install -popd - -pushd mpc-src -./configure --disable-shared --enable-static \ - --prefix="$SRC_DIR/mpc-build" \ - --with-gmp="$SRC_DIR/gmp-build" \ - --with-mpfr="$SRC_DIR/mpfr-build" - -make -j $n && make check && make install -popd - -pushd gcc-src -./configure --prefix="$PREFIX" \ - --enable-checking=release \ - --with-arch=x86-64 \ - --disable-multilib \ - --enable-libgomp \ - --enable-languages=c,c++,fortran \ - --with-gmp="$SRC_DIR/gmp-build" \ - --with-mpfr="$SRC_DIR/mpfr-build" \ - --with-mpc="$SRC_DIR/mpc-build" - -make -j $n && make install -popd diff --git a/recipes/gcc_npg/4.6.4/meta.yaml b/recipes/gcc_npg/4.6.4/meta.yaml deleted file mode 100644 index 29605582..00000000 --- a/recipes/gcc_npg/4.6.4/meta.yaml +++ /dev/null @@ -1,72 +0,0 @@ -{% set version = "4.6.4" %} -{% set sha256 = "53de33db01815914b3905a7d2cefac1ecf24ad081b82d93e4f526d8e62ff736f" %} - -{% set gmp_version = "4.3.2" %} -{% set gmp_sha256 = "936162c0312886c21581002b79932829aa048cfaf9937c6265aeaa14f1cd1775" %} - -{% set mpfr_version = "2.4.2" %} -{% set mpfr_sha256 = "c7e75a08a8d49d2082e4caee1591a05d11b9d5627514e678f02d66a124bcf2ba" %} - -{% set mpc_version = "0.8.1" %} -{% set mpc_sha256 = "e664603757251fd8a352848276497a4c79b7f8b21fd8aedd5cc0598a38fee3e4" %} - -package: - name: gcc_npg - version: "{{ version }}" - -about: - home: https://gcc.gnu.org/ - license: GPLv3 - summary: The GNU Compiler Collection. - -build: - number: 1 - - rpaths: - - lib64 - - lib - -source: - - url: ftp://ftp.mirrorservice.org/sites/sourceware.org/pub/gcc/releases/gcc-{{ version }}/gcc-{{ version }}.tar.gz - fn: gcc-{{ version }}.tar.gz - folder: gcc-src - sha256: {{ sha256 }} - - - url: https://gmplib.org/download/gmp/archive/gmp-{{ gmp_version }}.tar.bz2 - fn: gmp-{{ gmp_version }}.tar.bz2 - folder: gmp-src - sha256: {{ gmp_sha256 }} - - - url: http://www.mpfr.org/mpfr-{{ mpfr_version }}/mpfr-{{ mpfr_version }}.tar.bz2 - fn: mpfr-{{ mpfr_version }}.tar.bz2 - folder: mpfr-src - sha256: {{ mpfr_sha256 }} - - - url: http://www.multiprecision.org/downloads/mpc-{{ mpc_version }}.tar.gz - fn: mpc-{{ mpc_version }}.tar.gz - folder: mpc-src - sha256: {{ mpc_sha256 }} - -outputs: - - name: gcc_npg - version: {{ version }} - requirements: - run: - - libgcc_npg =={{ version }} - files: - - bin/c++ - - bin/g++ - - bin/cpp - - bin/gfortran - - bin/gcc* - - bin/gcov* - - bin/x86_64* - - include - - lib - - libexec - - share - - - name: libgcc_npg - version: {{ version }} - files: - - lib64 diff --git a/recipes/gcc_npg/5.5.0/build.sh b/recipes/gcc_npg/5.5.0/build.sh deleted file mode 100755 index 84871233..00000000 --- a/recipes/gcc_npg/5.5.0/build.sh +++ /dev/null @@ -1,58 +0,0 @@ -#!/bin/sh - -set -e - -n=$CPU_COUNT - -for pkg in gmp mpfr mpc isl gcc; do - mkdir -p "$SRC_DIR/$pkg-build" -done - -pushd gmp-src -./configure --disable-shared --enable-static \ - --prefix="$SRC_DIR/gmp-build" \ - CFLAGS="-O2 -pedantic -fomit-frame-pointer -m64 -march=x86-64" \ - MPN_PATH="x86_64 generic" - -make -j $n && make check && make install -popd - -pushd mpfr-src -./configure --disable-shared --enable-static \ - --prefix="$SRC_DIR/mpfr-build" \ - --with-gmp="$SRC_DIR/gmp-build" - -make -j $n && make check && make install -popd - -pushd mpc-src -./configure --disable-shared --enable-static \ - --prefix="$SRC_DIR/mpc-build" \ - --with-gmp="$SRC_DIR/gmp-build" \ - --with-mpfr="$SRC_DIR/mpfr-build" - -make -j $n && make check && make install -popd - -pushd isl-src -./configure --disable-shared --enable-static \ - --prefix="$SRC_DIR/isl-build" \ - --with-gmp-prefix="$SRC_DIR/gmp-build" - -make -j $n && make install -popd - -pushd gcc-src -./configure --prefix="$PREFIX" \ - --enable-checking=release \ - --with-arch=x86-64 \ - --disable-multilib \ - --enable-libgomp \ - --enable-languages=c,c++,fortran \ - --with-gmp="$SRC_DIR/gmp-build" \ - --with-mpfr="$SRC_DIR/mpfr-build" \ - --with-mpc="$SRC_DIR/mpc-build" \ - --with-isl="$SRC_DIR/isl-build" - -make -j $n && make install -popd diff --git a/recipes/gcc_npg/5.5.0/meta.yaml b/recipes/gcc_npg/5.5.0/meta.yaml deleted file mode 100644 index de4890ab..00000000 --- a/recipes/gcc_npg/5.5.0/meta.yaml +++ /dev/null @@ -1,80 +0,0 @@ -{% set version = "5.5.0" %} -{% set sha256 = "3aabce75d6dd206876eced17504b28d47a724c2e430dbd2de176beb948708983" %} - -{% set gmp_version = "4.3.2" %} -{% set gmp_sha256 = "936162c0312886c21581002b79932829aa048cfaf9937c6265aeaa14f1cd1775" %} - -{% set mpfr_version = "2.4.2" %} -{% set mpfr_sha256 = "c7e75a08a8d49d2082e4caee1591a05d11b9d5627514e678f02d66a124bcf2ba" %} - -{% set mpc_version = "0.8.1" %} -{% set mpc_sha256 = "e664603757251fd8a352848276497a4c79b7f8b21fd8aedd5cc0598a38fee3e4" %} - -{% set isl_version = "0.15" %} -{% set isl_sha256 = "8ceebbf4d9a81afa2b4449113cee4b7cb14a687d7a549a963deb5e2a41458b6b" %} - -package: - name: gcc_npg - version: "{{ version }}" - -about: - home: https://gcc.gnu.org/ - license: GPLv3 - summary: The GNU Compiler Collection. - -build: - number: 1 - - rpaths: - - lib64 - - lib - -source: - - url: ftp://ftp.mirrorservice.org/sites/sourceware.org/pub/gcc/releases/gcc-{{ version }}/gcc-{{ version }}.tar.gz - fn: gcc-{{ version }}.tar.gz - folder: gcc-src - sha256: {{ sha256 }} - - - url: https://gmplib.org/download/gmp/archive/gmp-{{ gmp_version }}.tar.bz2 - fn: gmp-{{ gmp_version }}.tar.bz2 - folder: gmp-src - sha256: {{ gmp_sha256 }} - - - url: http://www.mpfr.org/mpfr-{{ mpfr_version }}/mpfr-{{ mpfr_version }}.tar.bz2 - fn: mpfr-{{ mpfr_version }}.tar.bz2 - folder: mpfr-src - sha256: {{ mpfr_sha256 }} - - - url: http://www.multiprecision.org/downloads/mpc-{{ mpc_version }}.tar.gz - fn: mpc-{{ mpc_version }}.tar.gz - folder: mpc-src - sha256: {{ mpc_sha256 }} - - - url: ftp://gcc.gnu.org/pub/gcc/infrastructure/isl-{{ isl_version }}.tar.bz2 - fn: isl-{{ isl_version }}.tar.bz2 - folder: isl-src - sha256: {{ isl_sha256 }} - -outputs: - - name: gcc_npg - version: {{ version }} - requirements: - run: - - libgcc_npg =={{ version }} - files: - - bin/c++ - - bin/g++ - - bin/cpp - - bin/gfortran - - bin/gcc* - - bin/gcov* - - bin/x86_64* - - include - - lib - - libexec - - share - - - name: libgcc_npg - version: {{ version }} - files: - - lib64 diff --git a/recipes/gcc_npg/7.3.0/build.sh b/recipes/gcc_npg/7.3.0/build.sh deleted file mode 100755 index 84871233..00000000 --- a/recipes/gcc_npg/7.3.0/build.sh +++ /dev/null @@ -1,58 +0,0 @@ -#!/bin/sh - -set -e - -n=$CPU_COUNT - -for pkg in gmp mpfr mpc isl gcc; do - mkdir -p "$SRC_DIR/$pkg-build" -done - -pushd gmp-src -./configure --disable-shared --enable-static \ - --prefix="$SRC_DIR/gmp-build" \ - CFLAGS="-O2 -pedantic -fomit-frame-pointer -m64 -march=x86-64" \ - MPN_PATH="x86_64 generic" - -make -j $n && make check && make install -popd - -pushd mpfr-src -./configure --disable-shared --enable-static \ - --prefix="$SRC_DIR/mpfr-build" \ - --with-gmp="$SRC_DIR/gmp-build" - -make -j $n && make check && make install -popd - -pushd mpc-src -./configure --disable-shared --enable-static \ - --prefix="$SRC_DIR/mpc-build" \ - --with-gmp="$SRC_DIR/gmp-build" \ - --with-mpfr="$SRC_DIR/mpfr-build" - -make -j $n && make check && make install -popd - -pushd isl-src -./configure --disable-shared --enable-static \ - --prefix="$SRC_DIR/isl-build" \ - --with-gmp-prefix="$SRC_DIR/gmp-build" - -make -j $n && make install -popd - -pushd gcc-src -./configure --prefix="$PREFIX" \ - --enable-checking=release \ - --with-arch=x86-64 \ - --disable-multilib \ - --enable-libgomp \ - --enable-languages=c,c++,fortran \ - --with-gmp="$SRC_DIR/gmp-build" \ - --with-mpfr="$SRC_DIR/mpfr-build" \ - --with-mpc="$SRC_DIR/mpc-build" \ - --with-isl="$SRC_DIR/isl-build" - -make -j $n && make install -popd diff --git a/recipes/gcc_npg/7.3.0/meta.yaml b/recipes/gcc_npg/7.3.0/meta.yaml deleted file mode 100644 index 6ca07b5e..00000000 --- a/recipes/gcc_npg/7.3.0/meta.yaml +++ /dev/null @@ -1,80 +0,0 @@ -{% set version = "7.3.0" %} -{% set sha256 = "fa06e455ca198ddc11ea4ddf2a394cf7cfb66aa7e0ab98cc1184189f1d405870" %} - -{% set gmp_version = "6.1.0" %} -{% set gmp_sha256 = "498449a994efeba527885c10405993427995d3f86b8768d8cdf8d9dd7c6b73e8" %} - -{% set mpfr_version = "3.1.4" %} -{% set mpfr_sha256 = "d3103a80cdad2407ed581f3618c4bed04e0c92d1cf771a65ead662cc397f7775" %} - -{% set mpc_version = "1.0.3" %} -{% set mpc_sha256 = "617decc6ea09889fb08ede330917a00b16809b8db88c29c31bfbb49cbf88ecc3" %} - -{% set isl_version = "0.16.1" %} -{% set isl_sha256 = "412538bb65c799ac98e17e8cfcdacbb257a57362acfaaff254b0fcae970126d2" %} - -package: - name: gcc_npg - version: "{{ version }}" - -about: - home: https://gcc.gnu.org/ - license: GPLv3 - summary: The GNU Compiler Collection. - -build: - number: 1 - - rpaths: - - lib64 - - lib - -source: - - url: ftp://ftp.mirrorservice.org/sites/sourceware.org/pub/gcc/releases/gcc-{{ version }}/gcc-{{ version }}.tar.gz - fn: gcc-{{ version }}.tar.gz - folder: gcc-src - sha256: {{ sha256 }} - - - url: https://gmplib.org/download/gmp/gmp-{{ gmp_version }}.tar.bz2 - fn: gmp-{{ gmp_version }}.tar.bz2 - folder: gmp-src - sha256: {{ gmp_sha256 }} - - - url: http://www.mpfr.org/mpfr-{{ mpfr_version }}/mpfr-{{ mpfr_version }}.tar.bz2 - fn: mpfr-{{ mpfr_version }}.tar.bz2 - folder: mpfr-src - sha256: {{ mpfr_sha256 }} - - - url: http://www.multiprecision.org/downloads/mpc-{{ mpc_version }}.tar.gz - fn: mpc-{{ mpc_version }}.tar.gz - folder: mpc-src - sha256: {{ mpc_sha256 }} - - - url: ftp://gcc.gnu.org/pub/gcc/infrastructure/isl-{{ isl_version }}.tar.bz2 - fn: isl-{{ isl_version }}.tar.bz2 - folder: isl-src - sha256: {{ isl_sha256 }} - -outputs: - - name: gcc_npg - version: {{ version }} - requirements: - run: - - libgcc_npg =={{ version }} - files: - - bin/c++ - - bin/g++ - - bin/cpp - - bin/gfortran - - bin/gcc* - - bin/gcov* - - bin/x86_64* - - include - - lib - - libexec - - share - - - name: libgcc_npg - version: {{ version }} - files: - - lib64 diff --git a/recipes/hdf5/1.8.20/build.sh b/recipes/hdf5/1.8.20/build.sh deleted file mode 100755 index edd70785..00000000 --- a/recipes/hdf5/1.8.20/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/sh - -set -e - -n=`expr $CPU_COUNT / 4 \| 1` - -./configure --prefix="$PREFIX" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" - -make -j $n -make install prefix="$PREFIX" diff --git a/recipes/hdf5/1.8.20/meta.yaml b/recipes/hdf5/1.8.20/meta.yaml deleted file mode 100644 index 972f75d7..00000000 --- a/recipes/hdf5/1.8.20/meta.yaml +++ /dev/null @@ -1,70 +0,0 @@ -{% set version = "1.8.20" %} -{% set short_version = "1.8" %} -{% set sha256 = "a4f2db7e0a078aa324f64e0216a80731731f73025367fa94d158c9b1d3fbdf6f" %} - -package: - name: hdf5 - version: "{{ version }}" - -about: - home: https://support.hdfgroup.org/HDF5/ - license: BSD - summary: A data model, library, and file format for storing and managing data. - -build: - number: 1 - string: threadsafe_{{ PKG_BUILDNUM }} - -source: - url: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-{{ short_version }}/hdf5-{{ version }}/src/hdf5-{{ version }}.tar.bz2 - fn: hdf5-{{ version }}.tar.gz - sha256: {{ sha256 }} - -requirements: - build: - - gcc_npg >=7.3 - - zlib - -outputs: - - name: hdf5 - version: {{ version }} - requirements: - run: - - libhdf5 =={{ version }} - files: - - bin/gif2h5 - - bin/h52gif - - bin/h5cc - - bin/h5copy - - bin/h5debug - - bin/h5diff - - bin/h5dump - - bin/h5import - - bin/h5jam - - bin/h5ls - - bin/h5mkgrp - - bin/h5perf_serial - - bin/h5redeploy - - bin/h5repack - - bin/h5repart - - bin/h5stat - - bin/h5unjam - test: - commands: - - h5dump -h - - - name: libhdf5 - version: {{ version }} - requirements: - run: - - zlib - files: - - include/H5* - - include/hdf5* - - lib/libhdf* - - share/hdf5_examples - test: - commands: - - test -f ${PREFIX}/include/hdf5.h - - test -f ${PREFIX}/lib/libhdf5.a - - test -h ${PREFIX}/lib/libhdf5.so diff --git a/recipes/htslib/1.5/build.sh b/recipes/htslib/1.5/build.sh deleted file mode 100755 index 3fbb57e8..00000000 --- a/recipes/htslib/1.5/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/bin/sh - -set -e - -n=`expr $CPU_COUNT / 4 \| 1` - -./configure --prefix="$PREFIX" --enable-libcurl CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make -j $n prefix="$PREFIX" -make install prefix="$PREFIX" - -cd ./plugins -make install prefix="$PREFIX" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" IRODS_HOME="$PREFIX" diff --git a/recipes/htslib/1.5/meta.yaml b/recipes/htslib/1.5/meta.yaml deleted file mode 100644 index 9071d26a..00000000 --- a/recipes/htslib/1.5/meta.yaml +++ /dev/null @@ -1,79 +0,0 @@ -{% set version = "1.5" %} -{% set plugins_rev = "201712" %} -{% set sha256 = "a02b515ea51d86352b089c63d778fb5e8b9d784937cf157e587189cb97ad922d" %} - -package: - name: htslib - version: "{{ version }}" - -about: - home: https://github.com/samtools/htslib - license: MIT - summary: C library for high-throughput sequencing data formats. - -build: - number: 5 - string: plugins_{{ plugins_rev }}_{{ PKG_BUILDNUM }} - -source: - - url: https://github.com/samtools/htslib/releases/download/{{ version }}/htslib-{{ version }}.tar.bz2 - fn: htslib-{{ version }}.tar.bz2 - sha256: {{ sha256 }} - - git_url: https://github.com/samtools/htslib-plugins.git - git_rev: {{ plugins_rev }} - folder: plugins - -features: - - irods - -requirements: - build: - - libbzip2 - - libcurl - - gcc_npg >=7.3 - - irods-dev # for plugins - - liblzma - - openssl - - zlib - -outputs: - - name: htsbin - version: {{ version }} - requirements: - run: - - htslib =={{ version }} - - libbzip2 - - libcurl - - liblzma - - openssl - - zlib - files: - - bin/bgzip - - bin/htsfile - - bin/tabix - - share/man/man1/htsfile.1 - - share/man/man1/tabix.1 - - - name: htslib - version: {{ version }} - requirements: - run: - - libbzip2 - - libcurl - - liblzma - - openssl - - zlib - files: - - include/htslib - - libexec/htslib - - lib/libhts* - - share/man/man5/faidx.5 - - share/man/man5/sam.5 - - share/man/man5/vcf.5 - - test: - commands: - - test -f ${PREFIX}/include/htslib/sam.h - - test -f ${PREFIX}/lib/libhts.a - - test -h ${PREFIX}/lib/libhts.so - - test -f ${PREFIX}/libexec/htslib/hfile_irods.so diff --git a/recipes/htslib/1.6/build.sh b/recipes/htslib/1.6/build.sh deleted file mode 100755 index c0ca2ffb..00000000 --- a/recipes/htslib/1.6/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/bin/sh - -set -e - -n=`expr $CPU_COUNT / 4 \| 1` - -./configure --prefix="$PREFIX" --enable-libcurl --enable-plugins CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make -j $n prefix="$PREFIX" -make install prefix="$PREFIX" - -cd ./plugins -make install prefix="$PREFIX" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" IRODS_HOME="$PREFIX" diff --git a/recipes/htslib/1.6/meta.yaml b/recipes/htslib/1.6/meta.yaml deleted file mode 100644 index 76fac264..00000000 --- a/recipes/htslib/1.6/meta.yaml +++ /dev/null @@ -1,80 +0,0 @@ -{% set version = "1.6" %} -{% set plugins_rev = "201712" %} -{% set sha256 = "9588be8be0c2390a87b7952d644e7a88bead2991b3468371347965f2e0504ccb" %} - -package: - name: htslib - version: "{{ version }}" - -about: - home: https://github.com/samtools/htslib - license: MIT - summary: C library for high-throughput sequencing data formats. - -build: - number: 5 - string: plugins_{{ plugins_rev }}_{{ PKG_BUILDNUM }} - -source: - - url: https://github.com/samtools/htslib/releases/download/{{ version }}/htslib-{{ version }}.tar.bz2 - fn: htslib-{{ version }}.tar.bz2 - sha256: {{ sha256 }} - - git_url: https://github.com/samtools/htslib-plugins.git - git_rev: {{ plugins_rev }} - folder: plugins - -features: - - irods - -requirements: - build: - - libbzip2 - - libcurl - - gcc_npg >=7.3 - - irods-dev # for plugins - - liblzma - - openssl - - zlib - -outputs: - - name: htsbin - version: {{ version }} - requirements: - run: - - htslib =={{ version }} - - libbzip2 - - libcurl - - liblzma - - openssl - - zlib - files: - - bin/bgzip - - bin/htsfile - - bin/tabix - - share/man/man1/htsfile.1 - - share/man/man1/tabix.1 - - - name: htslib - version: {{ version }} - requirements: - run: - - libbzip2 - - libcurl - - liblzma - - openssl - - zlib - files: - - include/htslib - - libexec/htslib - - lib/libhts* - - share/man/man5/faidx.5 - - share/man/man5/sam.5 - - share/man/man5/vcf.5 - - test: - commands: - - test -f ${PREFIX}/include/htslib/sam.h - - test -f ${PREFIX}/lib/libhts.a - - test -h ${PREFIX}/lib/libhts.so - - test -f ${PREFIX}/libexec/htslib/hfile_irods.so - - test -f ${PREFIX}/libexec/htslib/hfile_libcurl.so diff --git a/recipes/htslib/1.7/build.sh b/recipes/htslib/1.7/build.sh deleted file mode 100755 index 937ff346..00000000 --- a/recipes/htslib/1.7/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/bin/sh - -set -e - -n=`expr $CPU_COUNT / 4 \| 1` - -./configure --prefix="$PREFIX" --enable-libcurl --enable-plugins CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make -j $n -make install prefix="$PREFIX" - -cd ./plugins -make install prefix="$PREFIX" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" IRODS_HOME="$PREFIX" diff --git a/recipes/htslib/1.7/meta.yaml b/recipes/htslib/1.7/meta.yaml deleted file mode 100644 index 5c3b69c6..00000000 --- a/recipes/htslib/1.7/meta.yaml +++ /dev/null @@ -1,80 +0,0 @@ -{% set version = "1.7" %} -{% set plugins_rev = "201712" %} -{% set sha256 = "be3d4e25c256acdd41bebb8a7ad55e89bb18e2fc7fc336124b1e2c82ae8886c6" %} - -package: - name: "htslib" - version: "{{ version }}" - -about: - home: https://github.com/samtools/htslib - license: MIT - summary: C library for high-throughput sequencing data formats. - -build: - number: 5 - string: plugins_{{ plugins_rev }}_{{ PKG_BUILDNUM }} - -source: - - url: https://github.com/samtools/htslib/releases/download/{{ version }}/htslib-{{ version }}.tar.bz2 - fn: htslib-{{ version }}.tar.bz2 - sha256: {{ sha256 }} - - git_url: https://github.com/samtools/htslib-plugins.git - git_rev: {{ plugins_rev }} - folder: plugins - -features: - - irods - -requirements: - build: - - libbzip2 - - libcurl - - gcc_npg >=7.3 - - irods-dev # for plugins - - liblzma - - openssl - - zlib - -outputs: - - name: htsbin - version: {{ version }} - requirements: - run: - - htslib =={{ version }} - - libbzip2 - - libcurl - - liblzma - - openssl - - zlib - files: - - bin/bgzip - - bin/htsfile - - bin/tabix - - share/man/man1/htsfile.1 - - share/man/man1/tabix.1 - - - name: htslib - version: {{ version }} - requirements: - run: - - libbzip2 - - libcurl - - liblzma - - openssl - - zlib - files: - - include/htslib - - libexec/htslib - - lib/libhts* - - share/man/man5/faidx.5 - - share/man/man5/sam.5 - - share/man/man5/vcf.5 - - test: - commands: - - test -f ${PREFIX}/include/htslib/sam.h - - test -f ${PREFIX}/lib/libhts.a - - test -h ${PREFIX}/lib/libhts.so - - test -f ${PREFIX}/libexec/htslib/hfile_irods.so - - test -f ${PREFIX}/libexec/htslib/hfile_libcurl.so diff --git a/recipes/htslib/1.8+25-gc167fee/README.md b/recipes/htslib/1.8+25-gc167fee/README.md deleted file mode 100644 index b171a955..00000000 --- a/recipes/htslib/1.8+25-gc167fee/README.md +++ /dev/null @@ -1,3 +0,0 @@ -This post release build was created from the develop branch of htslib -to support a version of samtools having recent additions to samtools -stats. diff --git a/recipes/htslib/1.8+25-gc167fee/build.sh b/recipes/htslib/1.8+25-gc167fee/build.sh deleted file mode 100755 index 46f048c2..00000000 --- a/recipes/htslib/1.8+25-gc167fee/build.sh +++ /dev/null @@ -1,20 +0,0 @@ -#!/bin/sh - -set -e - -n=`expr $CPU_COUNT / 4 \| 1` - -pushd htslib -autoreconf -./configure --prefix="$PREFIX" \ - --enable-libcurl \ - --enable-plugins \ - CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make -j $n -make install prefix="$PREFIX" -popd - -pushd plugins -make install prefix="$PREFIX" IRODS_HOME="$PREFIX" \ - CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -popd diff --git a/recipes/htslib/1.8+25-gc167fee/meta.yaml b/recipes/htslib/1.8+25-gc167fee/meta.yaml deleted file mode 100644 index ba64fa61..00000000 --- a/recipes/htslib/1.8+25-gc167fee/meta.yaml +++ /dev/null @@ -1,80 +0,0 @@ -{% set version = "1.8+25_gc167fee" %} -{% set plugins_rev = "201712" %} -{% set htslib_rev = "c167feeaaa269e1739f462bc44ebd0307639853d" %} - -package: - name: "htslib" - version: "{{ version }}" - -about: - home: https://github.com/samtools/htslib - license: MIT - summary: C library for high-throughput sequencing data formats. - -build: - number: 0 - string: plugins_{{ plugins_rev }}_{{ PKG_BUILDNUM }} - -source: - - git_url: https://github.com/samtools/htslib.git - git_rev: {{ htslib_rev }} - folder: htslib - - git_url: https://github.com/samtools/htslib-plugins.git - git_rev: {{ plugins_rev }} - folder: plugins - -features: - - irods - -requirements: - build: - - libbzip2 - - libcurl - - gcc_npg >=7.3 - - irods-dev >=4.1.12 # for plugins - - liblzma - - openssl - - zlib - -outputs: - - name: htsbin - version: {{ version }} - requirements: - run: - - htslib =={{ version }} - - libbzip2 - - libcurl - - liblzma - - openssl - - zlib - files: - - bin/bgzip - - bin/htsfile - - bin/tabix - - share/man/man1/htsfile.1 - - share/man/man1/tabix.1 - - - name: htslib - version: {{ version }} - requirements: - run: - - libbzip2 - - libcurl - - liblzma - - openssl - - zlib - files: - - include/htslib - - libexec/htslib - - lib/libhts* - - share/man/man5/faidx.5 - - share/man/man5/sam.5 - - share/man/man5/vcf.5 - - test: - commands: - - test -f ${PREFIX}/include/htslib/sam.h - - test -f ${PREFIX}/lib/libhts.a - - test -h ${PREFIX}/lib/libhts.so - - test -f ${PREFIX}/libexec/htslib/hfile_irods.so - - test -f ${PREFIX}/libexec/htslib/hfile_libcurl.so diff --git a/recipes/htslib/1.8+48-g6cd9f24/README.md b/recipes/htslib/1.8+48-g6cd9f24/README.md deleted file mode 100644 index b171a955..00000000 --- a/recipes/htslib/1.8+48-g6cd9f24/README.md +++ /dev/null @@ -1,3 +0,0 @@ -This post release build was created from the develop branch of htslib -to support a version of samtools having recent additions to samtools -stats. diff --git a/recipes/htslib/1.8+48-g6cd9f24/build.sh b/recipes/htslib/1.8+48-g6cd9f24/build.sh deleted file mode 100755 index 46f048c2..00000000 --- a/recipes/htslib/1.8+48-g6cd9f24/build.sh +++ /dev/null @@ -1,20 +0,0 @@ -#!/bin/sh - -set -e - -n=`expr $CPU_COUNT / 4 \| 1` - -pushd htslib -autoreconf -./configure --prefix="$PREFIX" \ - --enable-libcurl \ - --enable-plugins \ - CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make -j $n -make install prefix="$PREFIX" -popd - -pushd plugins -make install prefix="$PREFIX" IRODS_HOME="$PREFIX" \ - CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -popd diff --git a/recipes/htslib/1.8+48-g6cd9f24/meta.yaml b/recipes/htslib/1.8+48-g6cd9f24/meta.yaml deleted file mode 100644 index 5e96a8ce..00000000 --- a/recipes/htslib/1.8+48-g6cd9f24/meta.yaml +++ /dev/null @@ -1,80 +0,0 @@ -{% set version = "1.8+48_g6cd9f24" %} -{% set plugins_rev = "201712" %} -{% set htslib_rev = "6cd9f2477d729896d78c3ee6e6eb5fd89c50d372" %} - -package: - name: "htslib" - version: "{{ version }}" - -about: - home: https://github.com/samtools/htslib - license: MIT - summary: C library for high-throughput sequencing data formats. - -build: - number: 0 - string: plugins_{{ plugins_rev }}_{{ PKG_BUILDNUM }} - -source: - - git_url: https://github.com/samtools/htslib.git - git_rev: {{ htslib_rev }} - folder: htslib - - git_url: https://github.com/samtools/htslib-plugins.git - git_rev: {{ plugins_rev }} - folder: plugins - -features: - - irods - -requirements: - build: - - libbzip2 - - libcurl - - gcc_npg >=7.3 - - irods-dev >=4.1.12 # for plugins - - liblzma - - openssl - - zlib - -outputs: - - name: htsbin - version: {{ version }} - requirements: - run: - - htslib =={{ version }} - - libbzip2 - - libcurl - - liblzma - - openssl - - zlib - files: - - bin/bgzip - - bin/htsfile - - bin/tabix - - share/man/man1/htsfile.1 - - share/man/man1/tabix.1 - - - name: htslib - version: {{ version }} - requirements: - run: - - libbzip2 - - libcurl - - liblzma - - openssl - - zlib - files: - - include/htslib - - libexec/htslib - - lib/libhts* - - share/man/man5/faidx.5 - - share/man/man5/sam.5 - - share/man/man5/vcf.5 - - test: - commands: - - test -f ${PREFIX}/include/htslib/sam.h - - test -f ${PREFIX}/lib/libhts.a - - test -h ${PREFIX}/lib/libhts.so - - test -f ${PREFIX}/libexec/htslib/hfile_irods.so - - test -f ${PREFIX}/libexec/htslib/hfile_libcurl.so diff --git a/recipes/htslib/1.8/build.sh b/recipes/htslib/1.8/build.sh deleted file mode 100755 index 04353fdc..00000000 --- a/recipes/htslib/1.8/build.sh +++ /dev/null @@ -1,16 +0,0 @@ -#!/bin/sh - -set -e - -n=`expr $CPU_COUNT / 4 \| 1` - -./configure --prefix="$PREFIX" \ - --enable-libcurl \ - --enable-plugins \ - CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make -j $n -make install prefix="$PREFIX" - -cd ./plugins -make install prefix="$PREFIX" IRODS_HOME="$PREFIX" \ - CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" \ diff --git a/recipes/htslib/1.8/meta.yaml b/recipes/htslib/1.8/meta.yaml deleted file mode 100644 index 12f61092..00000000 --- a/recipes/htslib/1.8/meta.yaml +++ /dev/null @@ -1,80 +0,0 @@ -{% set version = "1.8" %} -{% set plugins_rev = "201712" %} -{% set sha256 = "c0ef1eec954a98cc708e9f99f6037db85db45670b52b6ab37abcc89b6c057ca1" %} - -package: - name: "htslib" - version: "{{ version }}" - -about: - home: https://github.com/samtools/htslib - license: MIT - summary: C library for high-throughput sequencing data formats. - -build: - number: 3 - string: plugins_{{ plugins_rev }}_{{ PKG_BUILDNUM }} - -source: - - url: https://github.com/samtools/htslib/releases/download/{{ version }}/htslib-{{ version }}.tar.bz2 - fn: htslib-{{ version }}.tar.bz2 - sha256: {{ sha256 }} - - git_url: https://github.com/samtools/htslib-plugins.git - git_rev: {{ plugins_rev }} - folder: plugins - -features: - - irods - -requirements: - build: - - libbzip2 - - libcurl - - gcc_npg >=7.3 - - irods-dev >=4.1.12 # for plugins - - liblzma - - openssl - - zlib - -outputs: - - name: htsbin - version: {{ version }} - requirements: - run: - - htslib =={{ version }} - - libbzip2 - - libcurl - - liblzma - - openssl - - zlib - files: - - bin/bgzip - - bin/htsfile - - bin/tabix - - share/man/man1/htsfile.1 - - share/man/man1/tabix.1 - - - name: htslib - version: {{ version }} - requirements: - run: - - libbzip2 - - libcurl - - liblzma - - openssl - - zlib - files: - - include/htslib - - libexec/htslib - - lib/libhts* - - share/man/man5/faidx.5 - - share/man/man5/sam.5 - - share/man/man5/vcf.5 - - test: - commands: - - test -f ${PREFIX}/include/htslib/sam.h - - test -f ${PREFIX}/lib/libhts.a - - test -h ${PREFIX}/lib/libhts.so - - test -f ${PREFIX}/libexec/htslib/hfile_irods.so - - test -f ${PREFIX}/libexec/htslib/hfile_libcurl.so diff --git a/recipes/minimap2/2.8/Makefile.patch b/recipes/minimap2/2.8/Makefile.patch deleted file mode 100644 index 20a340af..00000000 --- a/recipes/minimap2/2.8/Makefile.patch +++ /dev/null @@ -1,15 +0,0 @@ ---- Makefile 2018-06-18 14:12:28.482950000 +0100 -+++ Makefile.1 2018-06-18 14:46:12.234408000 +0100 -@@ -29,10 +29,10 @@ - extra:all $(PROG_EXTRA) - - minimap2:main.o getopt.o libminimap2.a -- $(CC) $(CFLAGS) main.o getopt.o -o $@ -L. -lminimap2 $(LIBS) -+ $(CC) $(CFLAGS) main.o getopt.o -o $@ -L. $(LDFLAGS) -lminimap2 $(LIBS) - - minimap2-lite:example.o libminimap2.a -- $(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS) -+ $(CC) $(CFLAGS) $< -o $@ -L. $(LDFLAGS) -lminimap2 $(LIBS) - - libminimap2.a:$(OBJS) - $(AR) -csru $@ $(OBJS) diff --git a/recipes/minimap2/2.8/build.sh b/recipes/minimap2/2.8/build.sh deleted file mode 100755 index e7f8dbea..00000000 --- a/recipes/minimap2/2.8/build.sh +++ /dev/null @@ -1,13 +0,0 @@ -#!/bin/sh - -set -e - -n=`expr $CPU_COUNT / 4 \| 1` - -make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" - -mkdir -p "$PREFIX/bin" -cp minimap2 "$PREFIX/bin/" - -mkdir -p "$PREFIX/share/man/man1" -cp minimap2.1 "$PREFIX/share/man/man1/" diff --git a/recipes/minimap2/2.8/meta.yaml b/recipes/minimap2/2.8/meta.yaml deleted file mode 100644 index e10f2125..00000000 --- a/recipes/minimap2/2.8/meta.yaml +++ /dev/null @@ -1,33 +0,0 @@ -{% set version = "2.8" %} -{% set sha256 = "9899e548f4f4cbf2b9a5c3b20facb8dd583ee9f39be7ac0c3b0bdeb5ca3b0cc2" %} - -package: - name: minimap2 - version: "{{ version }}" - -about: - home: https://lh3.github.io/minimap2 - license: MIT - summary: "A versatile pairwise aligner for genomic and spliced nucleotide sequences." - -build: - number: 1 - -source: - url: https://github.com/lh3/minimap2/releases/download/v{{ version }}/minimap2-{{ version }}.tar.bz2 - sha256: {{ sha256 }} - - patches: - - Makefile.patch - -requirements: - build: - - gcc_npg >=7.3 - - zlib - - run: - - zlib - -test: - commands: - - minimap2 --version diff --git a/recipes/nanopolish/0.8.5/build.sh b/recipes/nanopolish/0.8.5/build.sh deleted file mode 100755 index f36f548e..00000000 --- a/recipes/nanopolish/0.8.5/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/bin/sh - -set -e - -git submodule update --init --recursive - -make EIGEN=noinstall HDF5=noinstall HTS=noinstall CXXFLAGS="-I$PREFIX/include -I$PREFIX/include/eigen3" LDFLAGS="-L$PREFIX/lib" - -# There is no install target in the Makefile -mkdir -p "$PREFIX/bin" - -cp nanopolish "$PREFIX/bin/" diff --git a/recipes/nanopolish/0.8.5/meta.yaml b/recipes/nanopolish/0.8.5/meta.yaml deleted file mode 100644 index bc6f5e1e..00000000 --- a/recipes/nanopolish/0.8.5/meta.yaml +++ /dev/null @@ -1,41 +0,0 @@ -{% set version = "0.8.5" %} - -package: - name: nanopolish - version: "{{ version }}" - -about: - home: https://github.com/jts/nanopolish - license: MIT - summary: "Software package for signal-level analysis of Oxford Nanopore sequencing data." - -build: - number: 1 - - rpaths: - - lib64 - - lib - -source: - git_url: https://github.com/jts/nanopolish.git - git_rev: v{{ version }} - patches: - - patch-build-system-htslib-gomp.patch - -requirements: - build: - - libbzip2 - - eigen - - gcc_npg >=7.3 - - hdf5 - - htslib >=1.7 - - liblzma - - zlib - - run: - - libbzip2 - - hdf5 - - htslib >=1.7 - - libgcc_npg >=7.3 - - liblzma - - zlib diff --git a/recipes/nanopolish/0.8.5/patch-build-system-htslib-gomp.patch b/recipes/nanopolish/0.8.5/patch-build-system-htslib-gomp.patch deleted file mode 100644 index 21034442..00000000 --- a/recipes/nanopolish/0.8.5/patch-build-system-htslib-gomp.patch +++ /dev/null @@ -1,53 +0,0 @@ -From 2af850f732400a8bf3728ce1104221804f8908f9 Mon Sep 17 00:00:00 2001 -From: Keith James -Date: Thu, 25 Jan 2018 10:24:09 +0000 -Subject: [PATCH 1/2] Fix building with system htslib. - ---- - Makefile | 4 +++- - 1 file changed, 3 insertions(+), 1 deletion(-) - -diff --git a/Makefile b/Makefile -index 3cab7a6..11eb580 100644 ---- a/Makefile -+++ b/Makefile -@@ -52,7 +52,9 @@ ifeq ($(HTS), install) - HTS_INCLUDE=-I./htslib - else - # Use system-wide htslib -- HTS_LIB=-lhts -+ HTS_LIB= -+ HTS_INCLUDE= -+ LIBS += -lhts - endif - - # Include the header-only fast5 library --- -1.7.9.5 - - -From 786e4576d2d8082f9804a3b655e149314d733dd3 Mon Sep 17 00:00:00 2001 -From: Keith James -Date: Thu, 25 Jan 2018 10:24:51 +0000 -Subject: [PATCH 2/2] Fixed omp linking. - ---- - Makefile | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/Makefile b/Makefile -index 11eb580..49d7627 100644 ---- a/Makefile -+++ b/Makefile -@@ -8,7 +8,7 @@ SUBDIRS := src src/hmm src/thirdparty src/thirdparty/scrappie src/common src/ali - # - - #Basic flags every build needs --LIBS=-lz -+LIBS=-lz -lgomp - CXXFLAGS ?= -g -O3 - CXXFLAGS += -std=c++11 -fopenmp -fsigned-char - CFLAGS ?= -O3 -std=c99 --- -1.7.9.5 - diff --git a/recipes/nodejs/6.12.2/build.sh b/recipes/nodejs/6.12.2/build.sh deleted file mode 100644 index 575864d2..00000000 --- a/recipes/nodejs/6.12.2/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/sh - -set -e - -./configure --prefix="$PREFIX" - -make -j 3 -make install - -PATH="$PREFIX/bin:$PATH" npm install -g npm@4.5.0 diff --git a/recipes/nodejs/6.12.2/meta.yaml b/recipes/nodejs/6.12.2/meta.yaml deleted file mode 100644 index 81eeafbb..00000000 --- a/recipes/nodejs/6.12.2/meta.yaml +++ /dev/null @@ -1,38 +0,0 @@ -{% set version = "6.12.2" %} -{% set sha256 = "1bb1d3a033d69ccfa4051ffa79bedad9bcfd43bc0d4b2b6678c3e53883bfd6eb" %} - -package: - name: nodejs - version: "{{ version }}" - -about: - home: https://nodejs.org - license: MIT - summary: "Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine." - -source: - url: https://nodejs.org/dist/v{{ version }}/node-v{{ version }}.tar.gz - fn: node-v{{ version }}-linux-x64.tar.gz - sha256: {{ sha256 }} - -build: - number: 1 - ignore_prefix_files: - - bin/node - -requirements: - build: - - python 2.7.* - - gcc_npg >=5.5 - - run: - - libgcc_npg - -test: - commands: - - node -h - - node -v - - npm version - - npm install -h - - npm config get prefix -g - - test $(echo "console.log(1 + 3)" | node) == 4 diff --git a/recipes/porechop/0.2.3/build.sh b/recipes/porechop/0.2.3/build.sh deleted file mode 100755 index c866cdb4..00000000 --- a/recipes/porechop/0.2.3/build.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/sh - -set -e - -python3 setup.py install --prefix="$PREFIX" diff --git a/recipes/porechop/0.2.3/meta.yaml b/recipes/porechop/0.2.3/meta.yaml deleted file mode 100644 index 0642cc68..00000000 --- a/recipes/porechop/0.2.3/meta.yaml +++ /dev/null @@ -1,35 +0,0 @@ -{% set version = "0.2.3" %} -{% set sha256 = "bfed39f82abc54f44fffd9b13d2121868084da7ac3d158ac9b9aa6fa0257f0f4" %} - -package: - name: porechop - version: "{{ version }}" - -about: - home: https://github.com/rrwick/Porechop - license: GPLv3 - summary: "Adapter trimmer for Oxford Nanopore reads." - -build: - number: 0 - - rpaths: - - lib64 - - lib - -source: - url: https://github.com/rrwick/Porechop/archive/v{{ version }}.tar.gz - sha256: {{ sha256 }} - -requirements: - build: - - gcc_npg >=5.5,<7.0.0 - - python >=3.4 - - run: - - python >=3.4 - - libgcc_npg >=5.5,<7.0.0 - -test: - commands: - - porechop --help diff --git a/recipes/samtools/1.5/build.sh b/recipes/samtools/1.5/build.sh deleted file mode 100755 index 35bcf73a..00000000 --- a/recipes/samtools/1.5/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/sh - -set -e - -n=`expr $CPU_COUNT / 4 \| 1` - -./configure --prefix="$PREFIX" --with-htslib=system --without-curses CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" - -make -j $n -make install prefix="$PREFIX" diff --git a/recipes/samtools/1.5/meta.yaml b/recipes/samtools/1.5/meta.yaml deleted file mode 100644 index aee09a6e..00000000 --- a/recipes/samtools/1.5/meta.yaml +++ /dev/null @@ -1,31 +0,0 @@ -{% set version = "1.5" %} -{% set sha256 = "8542da26832ee08c1978713f5f6188ff750635b50d8ab126a0c7bb2ac1ae2df6" %} - -package: - name: samtools - version: "{{ version }}" - -about: - home: https://github.com/samtools/samtools - license: MIT - summary: C library for high-throughput sequencing data formats. - -build: - number: 2 - -source: - url: https://github.com/samtools/samtools/releases/download/{{ version }}/samtools-{{ version }}.tar.bz2 - fn: samtools-{{ version }}.tar.bz2 - sha256: {{ sha256 }} - -requirements: - build: - - gcc_npg >=7.3 - - htslib =={{ version }} - - run: - - htslib =={{ version }} - -test: - commands: - - echo '@HD VN:1.0 SO:coordinate' | samtools view diff --git a/recipes/samtools/1.6/build.sh b/recipes/samtools/1.6/build.sh deleted file mode 100755 index 35bcf73a..00000000 --- a/recipes/samtools/1.6/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/sh - -set -e - -n=`expr $CPU_COUNT / 4 \| 1` - -./configure --prefix="$PREFIX" --with-htslib=system --without-curses CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" - -make -j $n -make install prefix="$PREFIX" diff --git a/recipes/samtools/1.6/meta.yaml b/recipes/samtools/1.6/meta.yaml deleted file mode 100644 index b60832e9..00000000 --- a/recipes/samtools/1.6/meta.yaml +++ /dev/null @@ -1,31 +0,0 @@ -{% set version = "1.6" %} -{% set sha256 = "ee5cd2c8d158a5969a6db59195ff90923c662000816cc0c41a190b2964dbe49e" %} - -package: - name: samtools - version: "{{ version }}" - -about: - home: https://github.com/samtools/samtools - license: MIT - summary: C library for high-throughput sequencing data formats. - -build: - number: 2 - -source: - url: https://github.com/samtools/samtools/releases/download/{{ version }}/samtools-{{ version }}.tar.bz2 - fn: samtools-{{ version }}.tar.bz2 - sha256: {{ sha256 }} - -requirements: - build: - - gcc_npg >=7.3 - - htslib =={{ version }} - - run: - - htslib =={{ version }} - -test: - commands: - - echo '@HD VN:1.0 SO:coordinate' | samtools view diff --git a/recipes/samtools/1.7/build.sh b/recipes/samtools/1.7/build.sh deleted file mode 100755 index 35bcf73a..00000000 --- a/recipes/samtools/1.7/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/sh - -set -e - -n=`expr $CPU_COUNT / 4 \| 1` - -./configure --prefix="$PREFIX" --with-htslib=system --without-curses CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" - -make -j $n -make install prefix="$PREFIX" diff --git a/recipes/samtools/1.7/meta.yaml b/recipes/samtools/1.7/meta.yaml deleted file mode 100644 index 89d0899a..00000000 --- a/recipes/samtools/1.7/meta.yaml +++ /dev/null @@ -1,31 +0,0 @@ -{% set version = "1.7" %} -{% set sha256 = "e7b09673176aa32937abd80f95f432809e722f141b5342186dfef6a53df64ca1" %} - -package: - name: samtools - version: "{{ version }}" - -about: - home: https://github.com/samtools/samtools - license: MIT - summary: C library for high-throughput sequencing data formats. - -build: - number: 2 - -source: - url: https://github.com/samtools/samtools/releases/download/{{ version }}/samtools-{{ version }}.tar.bz2 - fn: samtools-{{ version }}.tar.bz2 - sha256: {{ sha256 }} - -requirements: - build: - - gcc_npg >=7.3 - - htslib =={{ version }} - - run: - - htslib =={{ version }} - -test: - commands: - - echo '@HD VN:1.0 SO:coordinate' | samtools view diff --git a/recipes/samtools/1.8+27-g0896262/README.md b/recipes/samtools/1.8+27-g0896262/README.md deleted file mode 100644 index 9e7ec462..00000000 --- a/recipes/samtools/1.8+27-g0896262/README.md +++ /dev/null @@ -1,2 +0,0 @@ -This post release build was created from the develop branch of -samtools to include recent additions to samtools stats. diff --git a/recipes/samtools/1.8+27-g0896262/build.sh b/recipes/samtools/1.8+27-g0896262/build.sh deleted file mode 100755 index 70c84b14..00000000 --- a/recipes/samtools/1.8+27-g0896262/build.sh +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/sh - -set -e - -n=`expr $CPU_COUNT / 4 \| 1` - -autoreconf -./configure --prefix="$PREFIX" \ - --with-htslib=system \ - --without-curses \ - CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" - -make -j $n -make install prefix="$PREFIX" diff --git a/recipes/samtools/1.8+27-g0896262/meta.yaml b/recipes/samtools/1.8+27-g0896262/meta.yaml deleted file mode 100644 index b049fda6..00000000 --- a/recipes/samtools/1.8+27-g0896262/meta.yaml +++ /dev/null @@ -1,30 +0,0 @@ -{% set version = "1.8+27_g0896262" %} -{% set htslib_version = "1.8+25_gc167fee" %} - -package: - name: samtools - version: "{{ version }}" - -about: - home: https://github.com/samtools/samtools - license: MIT - summary: C library for high-throughput sequencing data formats. - -build: - number: 0 - -source: - git_url: https://github.com/samtools/samtools.git - git_rev: 089626256f93cae0a6da89580e924f07ffc853c6 - -requirements: - build: - - gcc_npg >=7.3 - - htslib =={{ htslib_version }} - - run: - - htslib =={{ htslib_version }} - -test: - commands: - - echo '@HD VN:1.0 SO:coordinate' | samtools view diff --git a/recipes/samtools/1.8+59-g4da22a9/README.md b/recipes/samtools/1.8+59-g4da22a9/README.md deleted file mode 100644 index 9e7ec462..00000000 --- a/recipes/samtools/1.8+59-g4da22a9/README.md +++ /dev/null @@ -1,2 +0,0 @@ -This post release build was created from the develop branch of -samtools to include recent additions to samtools stats. diff --git a/recipes/samtools/1.8+59-g4da22a9/build.sh b/recipes/samtools/1.8+59-g4da22a9/build.sh deleted file mode 100755 index 70c84b14..00000000 --- a/recipes/samtools/1.8+59-g4da22a9/build.sh +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/sh - -set -e - -n=`expr $CPU_COUNT / 4 \| 1` - -autoreconf -./configure --prefix="$PREFIX" \ - --with-htslib=system \ - --without-curses \ - CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" - -make -j $n -make install prefix="$PREFIX" diff --git a/recipes/samtools/1.8+59-g4da22a9/meta.yaml b/recipes/samtools/1.8+59-g4da22a9/meta.yaml deleted file mode 100644 index 865e9737..00000000 --- a/recipes/samtools/1.8+59-g4da22a9/meta.yaml +++ /dev/null @@ -1,30 +0,0 @@ -{% set version = "1.8+59_g4da22a9" %} -{% set htslib_version = "1.8+48-g6cd9f24" %} - -package: - name: samtools - version: "{{ version }}" - -about: - home: https://github.com/samtools/samtools - license: MIT - summary: C library for high-throughput sequencing data formats. - -build: - number: 0 - -source: - git_url: https://github.com/samtools/samtools.git - git_rev: 4da22a93ddee8d52953cd1b24af29e1d8904eb7e - -requirements: - build: - - gcc_npg >=7.3 - - htslib =={{ htslib_version }} - - run: - - htslib =={{ htslib_version }} - -test: - commands: - - echo '@HD VN:1.0 SO:coordinate' | samtools view diff --git a/recipes/samtools/1.8/build.sh b/recipes/samtools/1.8/build.sh deleted file mode 100755 index 980bd0ee..00000000 --- a/recipes/samtools/1.8/build.sh +++ /dev/null @@ -1,13 +0,0 @@ -#!/bin/sh - -set -e - -n=`expr $CPU_COUNT / 4 \| 1` - -./configure --prefix="$PREFIX" \ - --with-htslib=system \ - --without-curses \ - CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" - -make -j $n -make install prefix="$PREFIX" diff --git a/recipes/samtools/1.8/meta.yaml b/recipes/samtools/1.8/meta.yaml deleted file mode 100644 index 060f7355..00000000 --- a/recipes/samtools/1.8/meta.yaml +++ /dev/null @@ -1,31 +0,0 @@ -{% set version = "1.8" %} -{% set sha256 = "c942bc1d9b85fd1b05ea79c5afd2805d489cd36b2c2d8517462682a4d779be16" %} - -package: - name: samtools - version: "{{ version }}" - -about: - home: https://github.com/samtools/samtools - license: MIT - summary: C library for high-throughput sequencing data formats. - -build: - number: 0 - -source: - url: https://github.com/samtools/samtools/releases/download/{{ version }}/samtools-{{ version }}.tar.bz2 - fn: samtools-{{ version }}.tar.bz2 - sha256: {{ sha256 }} - -requirements: - build: - - gcc_npg >=7.3 - - htslib =={{ version }} - - run: - - htslib =={{ version }} - -test: - commands: - - echo '@HD VN:1.0 SO:coordinate' | samtools view diff --git a/recipes/staden_io_lib/1.14.6/build.sh b/recipes/staden_io_lib/1.14.6/build.sh deleted file mode 100755 index 00268e19..00000000 --- a/recipes/staden_io_lib/1.14.6/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/sh - -set -e - -n=`expr $CPU_COUNT / 4 \| 1` - -./configure --prefix="$PREFIX" --with-zlib="$PREFIX" --with-libcurl="$PREFIX" - -make -j $n -make install prefix="$PREFIX" diff --git a/recipes/staden_io_lib/1.14.6/meta.yaml b/recipes/staden_io_lib/1.14.6/meta.yaml deleted file mode 100644 index dfbcc1c1..00000000 --- a/recipes/staden_io_lib/1.14.6/meta.yaml +++ /dev/null @@ -1,141 +0,0 @@ -{% set version = "1.14.6" %} -{% set sha256 = "94f76bfb6abbe86c96e2b0bc7a52525821893526c9a077bf3896c5b653cdbcdb" %} - -package: - name: staden_io_lib - version: "{{ version }}" - -about: - home: https://sourceforge.net/projects/staden - license: BSD - summary: DNA sequence assembly, editing and analysis tools. - -build: - number: 5 - -source: - url: https://sourceforge.net/projects/staden/files/io_lib/{{ version }}/io_lib-{{ version }}.tar.gz/download - fn: io_lib-{{ version }}.tar.gz - sha256: {{ sha256 }} - -outputs: - - name: staden_io_lib - version: {{ version }} - requirements: - build: - - {{ compiler("c") }} - - automake - - libtool - - make - host: - - libbz2-dev - - libcurl-dev - - liblzma-dev - - libz-dev - run: - - {{ pin_subpackage("libstaden-read", exact=True) }} - - libbz2 - - libcurl - - liblzma - - libz - files: - - bin/append_sff - - bin/convert_trace - - bin/cram_dump - - bin/cram_filter - - bin/cram_index - - bin/cram_size - - bin/extract_fastq - - bin/extract_qual - - bin/extract_seq - - bin/get_comment - - bin/hash_exp - - bin/hash_extract - - bin/hash_list - - bin/hash_sff - - bin/hash_tar - - bin/index_tar - - bin/makeSCF - - bin/scf_dump - - bin/scf_info - - bin/scf_update - - bin/scram_flagstat - - bin/scram_merge - - bin/scram_pileup - - bin/scram_test - - bin/scramble - - bin/srf2fasta - - bin/srf2fastq - - bin/srf_dump_all - - bin/srf_extract_hash - - bin/srf_extract_linear - - bin/srf_filter - - bin/srf_index_hash - - bin/srf_info - - bin/srf_list - - bin/trace_dump - - bin/ztr_dump - - share/man/man1/scramble.1 - - share/man/man1/srf2fasta.1 - - share/man/man1/srf2fastq.1 - - share/man/man1/srf_index_hash.1 - - share/man/man1/srf_info.1 - - share/man/man1/srf_list.1 - test: - commands: - - scramble -h - - - name: libstaden-read - version: {{ version }} - requirements: - build: - - {{ compiler("c") }} - - automake - - libtool - - make - host: - - libbz2-dev - - libcurl-dev - - liblzma-dev - - libz-dev - run: - - libbz2 - - libcurl - - liblzma - - libz - files: - - lib/libstaden-read* - test: - commands: - - test -f ${PREFIX}/lib/libstaden-read.a - - test -h ${PREFIX}/lib/libstaden-read.so - - - name: libstaden-read-dev - version: {{ version }} - requirements: - run: - - {{ pin_subpackage("libstaden-read", exact=True) }} - files: - - bin/io_lib-config - - include/io_lib - - share/man/man3/ExperimentFile.3 - - share/man/man3/exp2read.3 - - share/man/man3/fread_reading.3 - - share/man/man3/fread_scf.3 - - share/man/man3/fwrite_reading.3 - - share/man/man3/fwrite_scf.3 - - share/man/man3/read2exp.3 - - share/man/man3/read2scf.3 - - share/man/man3/read_allocate.3 - - share/man/man3/read_deallocate.3 - - share/man/man3/read_reading.3 - - share/man/man3/read_scf.3 - - share/man/man3/read_scf_header.3 - - share/man/man3/scf2read.3 - - share/man/man3/write_reading.3 - - share/man/man3/write_scf.3 - - share/man/man3/write_scf_header.3 - - share/man/man4/Read.4 - test: - commands: - - test -f ${PREFIX}/include/io_lib/io_lib_config.h diff --git a/recipes/staden_io_lib/1.14.9/build.sh b/recipes/staden_io_lib/1.14.9/build.sh deleted file mode 100755 index c3d65d2b..00000000 --- a/recipes/staden_io_lib/1.14.9/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/sh - -set -ex - -n="$CPU_COUNT" - -./configure --prefix="$PREFIX" --with-zlib="$PREFIX" --with-libcurl="$PREFIX" - -make -j $n CPPFLAGS="-I$PREFIX/include" \ - LDFLAGS="-Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib" -make install prefix="$PREFIX" diff --git a/recipes/staden_io_lib/1.14.9/meta.yaml b/recipes/staden_io_lib/1.14.9/meta.yaml deleted file mode 100644 index 5ac66cde..00000000 --- a/recipes/staden_io_lib/1.14.9/meta.yaml +++ /dev/null @@ -1,141 +0,0 @@ -{% set version = "1.14.9" %} -{% set sha256 = "8d0732f3d37abba1633731bfacac5fd7f8172eccb1cef224e8ced904d3b242f4" %} - -package: - name: staden_io_lib - version: "{{ version }}" - -about: - home: https://sourceforge.net/projects/staden - license: BSD - summary: DNA sequence assembly, editing and analysis tools. - -build: - number: 5 - -source: - url: https://sourceforge.net/projects/staden/files/io_lib/{{ version }}/io_lib-{{ version }}.tar.gz/download - fn: io_lib-{{ version }}.tar.gz - sha256: {{ sha256 }} - -outputs: - - name: staden_io_lib - version: {{ version }} - requirements: - build: - - {{ compiler("c") }} - - automake - - libtool - - make - host: - - libbz2-dev - - libcurl-dev - - liblzma-dev - - libz-dev - run: - - {{ pin_subpackage("libstaden-read", exact=True) }} - - libbz2 - - libcurl - - liblzma - - libz - files: - - bin/append_sff - - bin/convert_trace - - bin/cram_dump - - bin/cram_filter - - bin/cram_index - - bin/cram_size - - bin/extract_fastq - - bin/extract_qual - - bin/extract_seq - - bin/get_comment - - bin/hash_exp - - bin/hash_extract - - bin/hash_list - - bin/hash_sff - - bin/hash_tar - - bin/index_tar - - bin/makeSCF - - bin/scf_dump - - bin/scf_info - - bin/scf_update - - bin/scram_flagstat - - bin/scram_merge - - bin/scram_pileup - - bin/scram_test - - bin/scramble - - bin/srf2fasta - - bin/srf2fastq - - bin/srf_dump_all - - bin/srf_extract_hash - - bin/srf_extract_linear - - bin/srf_filter - - bin/srf_index_hash - - bin/srf_info - - bin/srf_list - - bin/trace_dump - - bin/ztr_dump - - share/man/man1/scramble.1 - - share/man/man1/srf2fasta.1 - - share/man/man1/srf2fastq.1 - - share/man/man1/srf_index_hash.1 - - share/man/man1/srf_info.1 - - share/man/man1/srf_list.1 - test: - commands: - - scramble -h - - - name: libstaden-read - version: {{ version }} - requirements: - build: - - {{ compiler("c") }} - - automake - - libtool - - make - host: - - libbz2-dev - - libcurl-dev - - liblzma-dev - - libz-dev - run: - - libbz2 - - libcurl - - liblzma - - libz - files: - - lib/libstaden-read* - test: - commands: - - test -f ${PREFIX}/lib/libstaden-read.a - - test -h ${PREFIX}/lib/libstaden-read.so - - - name: libstaden-read-dev - version: {{ version }} - requirements: - run: - - {{ pin_subpackage("libstaden-read", exact=True) }} - files: - - bin/io_lib-config - - include/io_lib - - share/man/man3/ExperimentFile.3 - - share/man/man3/exp2read.3 - - share/man/man3/fread_reading.3 - - share/man/man3/fread_scf.3 - - share/man/man3/fwrite_reading.3 - - share/man/man3/fwrite_scf.3 - - share/man/man3/read2exp.3 - - share/man/man3/read2scf.3 - - share/man/man3/read_allocate.3 - - share/man/man3/read_deallocate.3 - - share/man/man3/read_reading.3 - - share/man/man3/read_scf.3 - - share/man/man3/read_scf_header.3 - - share/man/man3/scf2read.3 - - share/man/man3/write_reading.3 - - share/man/man3/write_scf.3 - - share/man/man3/write_scf_header.3 - - share/man/man4/Read.4 - test: - commands: - - test -f ${PREFIX}/include/io_lib/io_lib_config.h diff --git a/recipes/tears/1.2.3/build.sh b/recipes/tears/1.2.3/build.sh deleted file mode 100755 index 571d09cb..00000000 --- a/recipes/tears/1.2.3/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/sh - -set -e - -autoreconf -fi - -./configure --prefix="$PREFIX" --with-irods="$PREFIX" CPPFLAGS="-I$PREFIX/include -I$PREFIX/include/irods" LDFLAGS="-L$PREFIX/lib -L$PREFIX/lib/irods/externals" - -make -make install prefix="$PREFIX" diff --git a/recipes/tears/1.2.3/meta.yaml b/recipes/tears/1.2.3/meta.yaml deleted file mode 100644 index 76b0c391..00000000 --- a/recipes/tears/1.2.3/meta.yaml +++ /dev/null @@ -1,35 +0,0 @@ -{% set version = "1.2.3" %} - -package: - name: tears - version: "{{ version }}" - -about: - home: https://github.com/whitwham/tears - license: GPLv3 - summary: Stream files to and from iRODS. - -build: - number: 0 - -source: - git_url: https://github.com/whitwham/tears.git - git_rev: v{{ version }} - -features: - - irods - -requirements: - build: - - gcc_npg >=7.3 - - htslib >=1.7 - - irods-dev - - jansson - - run: - - htslib >=1.7 - - jansson - -test: - commands: - - test -x ${PREFIX}/bin/tears diff --git a/recipes/tophat2/2.0.14/build.sh b/recipes/tophat2/2.0.14/build.sh deleted file mode 100755 index 45dab8ee..00000000 --- a/recipes/tophat2/2.0.14/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/sh - -set -e - -n=1 - -# Using --with-boost avoids picking up /usr/lib boost, if present. -./configure --prefix="$PREFIX" --with-boost="$PREFIX" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" - -make -j $n -make install prefix="$PREFIX" diff --git a/recipes/tophat2/2.0.14/meta.yaml b/recipes/tophat2/2.0.14/meta.yaml deleted file mode 100644 index 56297e4b..00000000 --- a/recipes/tophat2/2.0.14/meta.yaml +++ /dev/null @@ -1,34 +0,0 @@ -{% set version = "2.0.14" %} -{% set sha256 = "547c5c9d127cbf7d61bc73c4251ff98a07d57e59b3718666a18b58acfb8fcfbf" %} - -package: - name: tophat2 - version: "{{ version }}" - -about: - home: http://ccb.jhu.edu/software/tophat/index.shtml - license: BSL - summary: Spliced read mapper for RNA-Seq. - -build: - number: 0 - -source: - url: http://ccb.jhu.edu/software/tophat/downloads/tophat-{{ version }}.tar.gz - fn: tophat2-{{ version }}.tar.gz - sha256: {{ sha256 }} - -requirements: - build: - - boost - - gcc_npg >=4.6,<5.0 - - zlib - - run: - - boost - - libgcc_npg >=4.6,<5.0 - - zlib - -test: - commands: - - tophat2 --version diff --git a/recipes/util-linux/2.32/build.sh b/recipes/util-linux/2.32/build.sh deleted file mode 100644 index 973b8bb6..00000000 --- a/recipes/util-linux/2.32/build.sh +++ /dev/null @@ -1,75 +0,0 @@ -#!/bin/sh - -set -e - -n=`expr $CPU_COUNT / 4 \| 1` - -./configure --prefix="$PREFIX" \ - --enable-libuuid \ - --enable-libuuid-force-uuidd \ - --disable-libblkid \ - --disable-libmount \ - --disable-libsmartcols \ - --disable-libfdisk \ - --disable-mount \ - --disable-losetup \ - --disable-zramctl \ - --disable-fsck \ - --disable-partx \ - --disable-uuidd \ - --disable-mountpoint \ - --disable-fallocate \ - --disable-unshare \ - --disable-nsenter \ - --disable-setpriv \ - --disable-eject \ - --disable-agetty \ - --disable-cramfs \ - --disable-bfs \ - --disable-minix \ - --disable-fdformat \ - --disable-hwclock \ - --disable-lslogins \ - --disable-wdctl \ - --disable-cal \ - --disable-logger \ - --disable-switch_root \ - --disable-pivot_root \ - --disable-lsmem \ - --disable-chmem \ - --disable-ipcrm \ - --disable-ipcs \ - --disable-rfkill \ - --disable-tunelp \ - --disable-kill \ - --disable-last \ - --disable-utmpdump \ - --disable-line \ - --disable-mesg \ - --disable-raw \ - --disable-rename \ - --disable-vipw \ - --disable-newgrp \ - --disable-chsh-only-listed \ - --disable-login \ - --disable-nologin \ - --disable-sulogin \ - --disable-su \ - --disable-runuser \ - --disable-ul \ - --disable-more \ - --disable-pg \ - --disable-setterm \ - --disable-schedutils \ - --disable-wall \ - --disable-bash-completion \ - --disable-pylibmount \ - --disable-pg-bell \ - --disable-use-tty-group \ - --disable-makeinstall-chown \ - --disable-makeinstall-setuid \ - --disable-colors-default \ - --without-python - -make -j $n -make install diff --git a/recipes/util-linux/2.32/meta.yaml b/recipes/util-linux/2.32/meta.yaml deleted file mode 100644 index bcbb72e4..00000000 --- a/recipes/util-linux/2.32/meta.yaml +++ /dev/null @@ -1,49 +0,0 @@ -{% set version = "2.32" %} -{% set sha256 = "ce43afee3182f1bddb0be83f68bd378770efb9b6fdd8f464333ff8e07903db56" %} - -package: - name: util-linux - version: "{{ version }}" - -about: - home: https://mirrors.edge.kernel.org/pub/linux/utils/util-linux - license: BSD - summary: "Linux utilities from kernel.org" - -build: - number: 0 - -source: - url: https://mirrors.edge.kernel.org/pub/linux/utils/util-linux/v{{ version }}/util-linux-{{ version }}.tar.gz - fn: util-linux-{{ version }}.tar.gz - sha256: {{ sha256 }} - -outputs: - - name: libuuid - version: {{ version }} - files: - - include/uuid.h - - lib/libuuid.a - - lib/libuuid.so - - lib/libuuid.so.1 - - lib/libuuid.so.1.3.0 - - share/man/man1/uuidgen.1 - - share/man/man3/uuid.3 - - share/man/man3/uuid_clear.3 - - share/man/man3/uuid_compare.3 - - share/man/man3/uuid_copy.3 - - share/man/man3/uuid_generate.3 - - share/man/man3/uuid_is_null.3 - - share/man/man3/uuid_parse.3 - - share/man/man3/uuid_time.3 - - share/man/man3/uuid_unparse.3 - -requirements: - build: - - gcc_npg >=7.3 - -test: - commands: - - test -f ${PREFIX}/include/uuid/uuid.h - - test -f ${PREFIX}/lib/libuuid.a - - test -h ${PREFIX}/lib/libuuid.so diff --git a/recipes/wr/0.11.0/build.sh b/recipes/wr/0.11.0/build.sh deleted file mode 100644 index f093a2c3..00000000 --- a/recipes/wr/0.11.0/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/bin/sh - -set -e - -mkdir -p "$PREFIX/bin" -cp wr "$PREFIX/bin/" - -mkdir -p "$PREFIX/etc" -cp wr_config.yml "$PREFIX/etc/" - -mkdir -p "$PREFIX/share/doc/wr" -cp README.md "$PREFIX/share/doc/wr/" diff --git a/recipes/wr/0.11.0/meta.yaml b/recipes/wr/0.11.0/meta.yaml deleted file mode 100644 index b6ad6efd..00000000 --- a/recipes/wr/0.11.0/meta.yaml +++ /dev/null @@ -1,24 +0,0 @@ -{% set version = "0.11.0" %} -{% set sha256 = "eaa92e6f53b65c1065efadddca79160dbdabd307283ef3337155d22c01081104" %} - -package: - name: wr - version: "{{ version }}" - -about: - home: https://github.com/VertebrateResequencing/wr - license: GPLv3 - summary: "High performance Workflow Runner." - -build: - number: 0 - binary_relocation: false - -source: - url: https://github.com/VertebrateResequencing/wr/releases/download/v{{ version }}/wr-linux-x86-64.zip - fn: wr-{{ version }}.zip - sha256: {{ sha256 }} - -test: - commands: - - wr -h diff --git a/recipes/wr/0.12.0/build.sh b/recipes/wr/0.12.0/build.sh deleted file mode 100644 index f093a2c3..00000000 --- a/recipes/wr/0.12.0/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/bin/sh - -set -e - -mkdir -p "$PREFIX/bin" -cp wr "$PREFIX/bin/" - -mkdir -p "$PREFIX/etc" -cp wr_config.yml "$PREFIX/etc/" - -mkdir -p "$PREFIX/share/doc/wr" -cp README.md "$PREFIX/share/doc/wr/" diff --git a/recipes/wr/0.12.0/meta.yaml b/recipes/wr/0.12.0/meta.yaml deleted file mode 100644 index 04f3706c..00000000 --- a/recipes/wr/0.12.0/meta.yaml +++ /dev/null @@ -1,24 +0,0 @@ -{% set version = "0.12.0" %} -{% set sha256 = "f45727e6fe004265befc10e517501c1dec5feae07f58ca6f4906bb25d2969fad" %} - -package: - name: wr - version: "{{ version }}" - -about: - home: https://github.com/VertebrateResequencing/wr - license: GPLv3 - summary: "High performance Workflow Runner." - -build: - number: 0 - binary_relocation: false - -source: - url: https://github.com/VertebrateResequencing/wr/releases/download/v{{ version }}/wr-linux-x86-64.zip - fn: wr-{{ version }}.zip - sha256: {{ sha256 }} - -test: - commands: - - wr -h diff --git a/recipes/wr/0.13.0/build.sh b/recipes/wr/0.13.0/build.sh deleted file mode 100644 index f093a2c3..00000000 --- a/recipes/wr/0.13.0/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/bin/sh - -set -e - -mkdir -p "$PREFIX/bin" -cp wr "$PREFIX/bin/" - -mkdir -p "$PREFIX/etc" -cp wr_config.yml "$PREFIX/etc/" - -mkdir -p "$PREFIX/share/doc/wr" -cp README.md "$PREFIX/share/doc/wr/" diff --git a/recipes/wr/0.13.0/meta.yaml b/recipes/wr/0.13.0/meta.yaml deleted file mode 100644 index c059f853..00000000 --- a/recipes/wr/0.13.0/meta.yaml +++ /dev/null @@ -1,24 +0,0 @@ -{% set version = "0.13.0" %} -{% set sha256 = "595e14148937c74e944f88f94c8cfad47c538e7718e754ab731e5405b5e015b0" %} - -package: - name: wr - version: "{{ version }}" - -about: - home: https://github.com/VertebrateResequencing/wr - license: GPLv3 - summary: "High performance Workflow Runner." - -build: - number: 0 - binary_relocation: false - -source: - url: https://github.com/VertebrateResequencing/wr/releases/download/v{{ version }}/wr-linux-x86-64.zip - fn: wr-{{ version }}.zip - sha256: {{ sha256 }} - -test: - commands: - - wr -h diff --git a/recipes/wr/0.14.0/build.sh b/recipes/wr/0.14.0/build.sh deleted file mode 100644 index f093a2c3..00000000 --- a/recipes/wr/0.14.0/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/bin/sh - -set -e - -mkdir -p "$PREFIX/bin" -cp wr "$PREFIX/bin/" - -mkdir -p "$PREFIX/etc" -cp wr_config.yml "$PREFIX/etc/" - -mkdir -p "$PREFIX/share/doc/wr" -cp README.md "$PREFIX/share/doc/wr/" diff --git a/recipes/wr/0.14.0/meta.yaml b/recipes/wr/0.14.0/meta.yaml deleted file mode 100644 index 98614571..00000000 --- a/recipes/wr/0.14.0/meta.yaml +++ /dev/null @@ -1,24 +0,0 @@ -{% set version = "0.14.0" %} -{% set sha256 = "d5e432eb91becd51c94e78e3cb555b3cecd9fab7a4bfa3f932577e9b41444abf" %} - -package: - name: wr - version: "{{ version }}" - -about: - home: https://github.com/VertebrateResequencing/wr - license: GPLv3 - summary: "High performance Workflow Runner." - -build: - number: 0 - binary_relocation: false - -source: - url: https://github.com/VertebrateResequencing/wr/releases/download/v{{ version }}/wr-linux-x86-64.zip - fn: wr-{{ version }}.zip - sha256: {{ sha256 }} - -test: - commands: - - wr -h diff --git a/recipes/wr/0.15.0/build.sh b/recipes/wr/0.15.0/build.sh deleted file mode 100644 index f093a2c3..00000000 --- a/recipes/wr/0.15.0/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/bin/sh - -set -e - -mkdir -p "$PREFIX/bin" -cp wr "$PREFIX/bin/" - -mkdir -p "$PREFIX/etc" -cp wr_config.yml "$PREFIX/etc/" - -mkdir -p "$PREFIX/share/doc/wr" -cp README.md "$PREFIX/share/doc/wr/" diff --git a/recipes/wr/0.15.0/meta.yaml b/recipes/wr/0.15.0/meta.yaml deleted file mode 100644 index db7a4bfb..00000000 --- a/recipes/wr/0.15.0/meta.yaml +++ /dev/null @@ -1,24 +0,0 @@ -{% set version = "0.15.0" %} -{% set sha256 = "19e0a9d0bb336d337f2f115c8d137624a6bd3864e8ba19a0ad13bf91409f940a" %} - -package: - name: wr - version: "{{ version }}" - -about: - home: https://github.com/VertebrateResequencing/wr - license: GPLv3 - summary: "High performance Workflow Runner." - -build: - number: 0 - binary_relocation: false - -source: - url: https://github.com/VertebrateResequencing/wr/releases/download/v{{ version }}/wr-linux-x86-64.zip - fn: wr-{{ version }}.zip - sha256: {{ sha256 }} - -test: - commands: - - wr -h From 7ad571d33c59e06879ebaf175e5803d0db67a01f Mon Sep 17 00:00:00 2001 From: Keith James Date: Fri, 14 Dec 2018 13:59:50 +0000 Subject: [PATCH 005/119] Added support for RHEL/CentOS. --- recipes/irods/4.1.12/build.sh | 100 +++++++++++++++++++++++++-------- recipes/irods/4.1.12/meta.yaml | 2 +- 2 files changed, 79 insertions(+), 23 deletions(-) diff --git a/recipes/irods/4.1.12/build.sh b/recipes/irods/4.1.12/build.sh index df2a1b78..d848a9c1 100644 --- a/recipes/irods/4.1.12/build.sh +++ b/recipes/irods/4.1.12/build.sh @@ -1,45 +1,101 @@ #!/bin/sh -set -e +set -ex -function untar_data() { +untar_data() { if [ -e data.tar.gz ]; then - tar xz --strip-components=2 --directory="$PREFIX" --exclude='*.o' --exclude-backups < data.tar.gz + tar xz --strip-components=2 --directory="$PREFIX" \ + --exclude='*.o' --exclude-backups < data.tar.gz elif [ -e data.tar.xz ]; then - tar xJ --strip-components=2 --directory="$PREFIX" --exclude='*.o' --exclude-backups < data.tar.xz + tar xJ --strip-components=2 --directory="$PREFIX" \ + --exclude='*.o' --exclude-backups < data.tar.xz fi } +unrpm_data() { + local rpm="$1" + mkdir -p ./tmp + pushd tmp + rpm2cpio ../"$rpm" | cpio --extract --make-directories + popd + tar cf - -C ./tmp . | tar xv --strip-components=2 --directory="$PREFIX" \ + --exclude='*.o' --exclude-backups + rm -r ./tmp +} + +install_gcc_ubuntu() { + sudo apt-get install -y g++ g++-4.8 gcc gcc-4.8 + + sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 100 + sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 100 + sudo update-alternatives --set gcc /usr/bin/gcc-4.8 + sudo update-alternatives --set g++ /usr/bin/g++-4.8 +} + +install_deps_ubuntu() { + sudo apt-get install -y autoconf automake help2man make \ + libtool-bin pkg-config texinfo + + sudo apt-get install -y libjson-perl python-dev + + sudo apt-get install -y libbz2-dev libcurl4-gnutls-dev \ + libfuse-dev libkrb5-dev libmysqlclient-dev libpam0g-dev \ + libssl-dev unixodbc-dev libxml2-dev zlib1g-dev +} + +# Requires: +# +# sudo subscription-manager register --org="..." --activationkey="..." +# sudo subscription-manager repos --enable rhel-7-server-extras-rpms +# sudo subscription-manager repos --enable rhel-7-server-supplementary-rpms +# sudo subscription-manager repos --enable rhel-7-server-optional-rpms + +install_gcc_rhel() { + sudo yum install -y gcc-c++ +} + +install_deps_rhel() { + sudo yum install -y help2man make rpm-build + + sudo yum install -y perl-JSON python-devel + + sudo yum install -y bzip2-devel curl-devel \ + fuse-devel krb5-devel pam-devel \ + openssl-devel unixODBC-devel libxml2-devel zlib-devel +} + export TERM=dumb git submodule init && git submodule update -sudo apt-get install -y g++ g++-4.8 gcc gcc-4.8 +if [ -f /etc/lsb-release ]; then + install_gcc_ubuntu + install_deps_ubuntu -sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 100 -sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 100 -sudo update-alternatives --set gcc /usr/bin/gcc-4.8 -sudo update-alternatives --set g++ /usr/bin/g++-4.8 + ./packaging/build.sh --verbose icat postgres + ./packaging/build.sh --verbose icommands -sudo apt-get install -y autoconf automake help2man make \ - libtool-bin pkg-config texinfo + cd build -sudo apt-get install -y libjson-perl python-dev + ar vx irods-icommands-4.1.12-64bit.deb + untar_data -sudo apt-get install -y libbz2-dev libcurl4-gnutls-dev \ - libfuse-dev libkrb5-dev libmysqlclient-dev libpam0g-dev \ - libssl-dev unixodbc-dev libxml2-dev zlib1g-dev + ar vx irods-dev-4.1.12-64bit.deb + untar_data +fi -./packaging/build.sh --verbose icat postgres -./packaging/build.sh --verbose icommands +if [ -f /etc/redhat-release ]; then + install_gcc_rhel + install_deps_rhel -cd build + ./packaging/build.sh --verbose icat postgres + ./packaging/build.sh --verbose icommands -ar vx irods-icommands-4.1.12-64bit.deb -untar_data + cd build -ar vx irods-dev-4.1.12-64bit.deb -untar_data + unrpm_data irods-icommands-4.1.12-64bit-centos5.rpm + unrpm_data irods-dev-4.1.12-64bit-centos5.rpm +fi # Fix all the absolute symlinks pointing to /usr/include perl -le 'use strict; use File::Basename; foreach (@ARGV) { if (my $f = readlink $_) { if ($f =~ m{^/usr/}sm) { unlink $_; symlink(basename($f), $_) } } }' $PREFIX/include/irods/*.hpp diff --git a/recipes/irods/4.1.12/meta.yaml b/recipes/irods/4.1.12/meta.yaml index 797f9056..216bf965 100644 --- a/recipes/irods/4.1.12/meta.yaml +++ b/recipes/irods/4.1.12/meta.yaml @@ -10,7 +10,7 @@ about: summary: "Open Source Data Management Software." build: - number: 1 + number: 2 source: git_url: https://github.com/irods/irods.git From 9b9293d4a585c0d0a6ac91f3e5177d1db4996571 Mon Sep 17 00:00:00 2001 From: Keith James Date: Fri, 14 Dec 2018 14:02:11 +0000 Subject: [PATCH 006/119] Added host and run attributes to the package root requirements because conda-build does not pick them up from the sub-package requirements (bug?). If the compiler requirement is declared in the sub-package requirements, it is ignored. Disabled building Python support. --- recipes/boost/1.68.0/build.sh | 2 +- recipes/boost/1.68.0/conda_build_config.yaml | 5 +++++ recipes/boost/1.68.0/meta.yaml | 11 +++++++++-- 3 files changed, 15 insertions(+), 3 deletions(-) create mode 100644 recipes/boost/1.68.0/conda_build_config.yaml diff --git a/recipes/boost/1.68.0/build.sh b/recipes/boost/1.68.0/build.sh index 181044d6..da5c509d 100644 --- a/recipes/boost/1.68.0/build.sh +++ b/recipes/boost/1.68.0/build.sh @@ -18,7 +18,7 @@ done [ $nullglob_enabled ] || shopt -u nullglob -./bootstrap.sh --prefix="$PREFIX" --with-toolset=gcc +./bootstrap.sh --prefix="$PREFIX" --with-toolset=gcc --without-python # The cxxflags and linkflags options are not well documented. They do # not appear in `./b2 --help` and are only mentioned in the HTML docs diff --git a/recipes/boost/1.68.0/conda_build_config.yaml b/recipes/boost/1.68.0/conda_build_config.yaml new file mode 100644 index 00000000..54d7f516 --- /dev/null +++ b/recipes/boost/1.68.0/conda_build_config.yaml @@ -0,0 +1,5 @@ +c_compiler_version: + - 5.4 + +cxx_compiler_version: + - 5.4 diff --git a/recipes/boost/1.68.0/meta.yaml b/recipes/boost/1.68.0/meta.yaml index 91fc082f..98205f07 100644 --- a/recipes/boost/1.68.0/meta.yaml +++ b/recipes/boost/1.68.0/meta.yaml @@ -12,7 +12,7 @@ about: summary: "Free peer-reviewed portable C++ source libraries." build: - number: 0 + number: 1 source: url: https://dl.bintray.com/boostorg/release/{{ version }}/source/boost_{{ alt_version }}.tar.bz2 @@ -22,8 +22,15 @@ source: requirements: build: - {{ compiler("cxx") }} + - make + host: + - libbz2-dev + - liblzma-dev + - libz-dev run: - - {{ pin_subpackage("libboost-dev", exact=True) }} + - libbz2 + - liblzma + - libz outputs: - name: libboost From 111e579e3f797be3a77651d13ba53d158c2fc551 Mon Sep 17 00:00:00 2001 From: Keith James Date: Fri, 14 Dec 2018 14:05:50 +0000 Subject: [PATCH 007/119] Added a requirement for Python 2. Using Python 3 causes a syntax error in the TopHat script. --- recipes/tophat2/2.1.1/meta.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/recipes/tophat2/2.1.1/meta.yaml b/recipes/tophat2/2.1.1/meta.yaml index f35f7e6b..a610e6b6 100644 --- a/recipes/tophat2/2.1.1/meta.yaml +++ b/recipes/tophat2/2.1.1/meta.yaml @@ -29,7 +29,10 @@ requirements: run: - libboost - libz + - python <3.0 test: + requires: + - python <3.0 commands: - tophat2 --version From 745bcb3942fd68e42e82ccc33524ec7b4b564bee Mon Sep 17 00:00:00 2001 From: Keith James Date: Fri, 14 Dec 2018 14:07:30 +0000 Subject: [PATCH 008/119] Added a missing build requirement of automake. --- recipes/jansson/2.1.0/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/jansson/2.1.0/meta.yaml b/recipes/jansson/2.1.0/meta.yaml index 130d60d3..3a5e6438 100644 --- a/recipes/jansson/2.1.0/meta.yaml +++ b/recipes/jansson/2.1.0/meta.yaml @@ -25,6 +25,7 @@ outputs: build: - {{ compiler("c") }} - autoconf + - automake - libtool - make - perl From 7e96799a611fea9dfeebed33606f60e60e86a3ff Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 7 Jan 2019 08:57:44 +0000 Subject: [PATCH 009/119] Added sub-package requirements to the package root requirements because conda-build does not pick them up from the sub-package definition. --- recipes/baton/1.1.0/meta.yaml | 21 ++++++++++++++++++++- 1 file changed, 20 insertions(+), 1 deletion(-) diff --git a/recipes/baton/1.1.0/meta.yaml b/recipes/baton/1.1.0/meta.yaml index 0a3df908..6f052d77 100644 --- a/recipes/baton/1.1.0/meta.yaml +++ b/recipes/baton/1.1.0/meta.yaml @@ -18,8 +18,27 @@ source: fn: baton-{{ version }}.tar.gz sha256: {{ sha256 }} +requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - libtool + - make + - perl + - pkg-config + host: + - irods-dev ==4.1.12 + - libjansson-dev + - libssl-dev + run: + - {{ pin_subpackage("libbaton", exact=True) }} + - irods-plugins ==4.1.12 + - libjansson + - libssl + outputs: - - name: baton + - name: baton-bin version: {{ version }} requirements: build: From ac23766b2bce33a9062c0f8abebd567923b2e883 Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 7 Jan 2019 09:27:31 +0000 Subject: [PATCH 010/119] Added sub-package requirements to the package root requirements because conda-build does not pick them up from the sub-package definition. Renamed the nettle sub-package to nettle-bin because of https://github.com/conda/conda-build/issues/3313 Added --libdir="$PREFIX/lib" to the configure invocation to ensure that the libraries go to lib on Red Hat. --- recipes/nettle/3.3/build.sh | 1 + recipes/nettle/3.3/meta.yaml | 16 ++++++++++++++-- 2 files changed, 15 insertions(+), 2 deletions(-) diff --git a/recipes/nettle/3.3/build.sh b/recipes/nettle/3.3/build.sh index b8d2e1b5..f2af63d0 100755 --- a/recipes/nettle/3.3/build.sh +++ b/recipes/nettle/3.3/build.sh @@ -5,6 +5,7 @@ set -ex n="$CPU_COUNT" ./configure --prefix="$PREFIX" \ + --libdir="$PREFIX/lib" \ --with-include-path="$PREFIX/include" \ --with-lib-path="$PREFIX/lib" diff --git a/recipes/nettle/3.3/meta.yaml b/recipes/nettle/3.3/meta.yaml index 76c98cd3..9a537494 100644 --- a/recipes/nettle/3.3/meta.yaml +++ b/recipes/nettle/3.3/meta.yaml @@ -11,15 +11,27 @@ about: summary: A low-level cryptographic library build: - number: 2 + number: 3 source: url: https://ftp.gnu.org/gnu/nettle/nettle-{{ version }}.tar.gz fn: nettle-{{ version }}.tar.gz sha256: {{ sha256 }} +requirements: + build: + - {{ compiler("c") }} + - libtool + - m4 + - make + - pkg-config + host: + - libgmp-dev >=6.0 + run: + - libgmp >=6.0 + outputs: - - name: nettle + - name: nettle-bin requirements: build: - {{ compiler("c") }} From 670c49b659d41a160def7477ab335ee68cf19451 Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 7 Jan 2019 09:34:47 +0000 Subject: [PATCH 011/119] Corrected --without-python to --without-libraries=python. --- recipes/boost/1.68.0/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/boost/1.68.0/build.sh b/recipes/boost/1.68.0/build.sh index da5c509d..10e17944 100644 --- a/recipes/boost/1.68.0/build.sh +++ b/recipes/boost/1.68.0/build.sh @@ -18,7 +18,7 @@ done [ $nullglob_enabled ] || shopt -u nullglob -./bootstrap.sh --prefix="$PREFIX" --with-toolset=gcc --without-python +./bootstrap.sh --prefix="$PREFIX" --with-toolset=gcc --without-libraries=python # The cxxflags and linkflags options are not well documented. They do # not appear in `./b2 --help` and are only mentioned in the HTML docs From d317ac6a8003e5b24142ba5727cb93895dc3728d Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 7 Jan 2019 09:41:01 +0000 Subject: [PATCH 012/119] Added sub-package requirements to the package root requirements because conda-build does not pick them up from the sub-package definition. Renamed the curl sub-package to curl-bin because of https://github.com/conda/conda-build/issues/3313 --- recipes/curl/7.58.0/meta.yaml | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/recipes/curl/7.58.0/meta.yaml b/recipes/curl/7.58.0/meta.yaml index cf753869..19fc2fe6 100644 --- a/recipes/curl/7.58.0/meta.yaml +++ b/recipes/curl/7.58.0/meta.yaml @@ -17,8 +17,21 @@ source: - url: http://curl.haxx.se/download/curl-{{ version }}.tar.bz2 sha256: {{ sha256 }} +requirements: + build: + - {{ compiler("c") }} + - make + host: + - libgnutls-dev + - libnettle-dev + - libz-dev + run: + - libgnutls + - libnettle + - libz + outputs: - - name: curl + - name: curl-bin version: {{ version }} requirements: build: From 2ca9ceb6a2ffb36590395b7f47ec5fda781d80a2 Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 7 Jan 2019 09:43:55 +0000 Subject: [PATCH 013/119] Added sub-package requirements to the package root requirements because conda-build does not pick them up from the sub-package definition. --- recipes/gmplib/6.1.2/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/gmplib/6.1.2/meta.yaml b/recipes/gmplib/6.1.2/meta.yaml index f9d27f5f..87ee3e64 100644 --- a/recipes/gmplib/6.1.2/meta.yaml +++ b/recipes/gmplib/6.1.2/meta.yaml @@ -21,8 +21,12 @@ source: requirements: build: - {{ compiler("c") }} + - m4 + - make + host: + - libz-dev run: - - {{ pin_subpackage("libgmp-dev", exact=True) }} + - libz outputs: - name: libgmp From f51ea265417fe588d5f33097f99eb155071dc82b Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 7 Jan 2019 09:45:09 +0000 Subject: [PATCH 014/119] Added sub-package requirements to the package root requirements because conda-build does not pick them up from the sub-package definition. Renamed the gnutls sub-package to gnutls-bin because of https://github.com/conda/conda-build/issues/3313 --- recipes/gnutls/3.4.17/meta.yaml | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/recipes/gnutls/3.4.17/meta.yaml b/recipes/gnutls/3.4.17/meta.yaml index 2fc4cae5..c5bcc0ab 100644 --- a/recipes/gnutls/3.4.17/meta.yaml +++ b/recipes/gnutls/3.4.17/meta.yaml @@ -19,8 +19,23 @@ source: fn: gnutls-{{ version }}.tar.xz sha256: {{ sha256 }} +requirements: + build: + - {{ compiler("c") }} + - libtool + - make + - pkg-config + host: + - libgmp-dev + - libnettle-dev + - libz-dev + run: + - libgmp + - libnettle + - libz + outputs: - - name: gnutls + - name: gnutls-bin version: {{ version }} requirements: build: From 5ef5f6173e5306534a075b0ee9881d1cfd96811b Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 7 Jan 2019 09:47:40 +0000 Subject: [PATCH 015/119] Added sub-package requirements to the package root requirements because conda-build does not pick them up from the sub-package definition. Renamed the htslib sub-package to htslib-bin because of https://github.com/conda/conda-build/issues/3313 --- recipes/htslib/1.9+47-gc93b673/meta.yaml | 26 +++++++++++++++++++++++- recipes/htslib/1.9+9-g6ec3b94/meta.yaml | 26 +++++++++++++++++++++++- 2 files changed, 50 insertions(+), 2 deletions(-) diff --git a/recipes/htslib/1.9+47-gc93b673/meta.yaml b/recipes/htslib/1.9+47-gc93b673/meta.yaml index fd333e96..a2cde097 100644 --- a/recipes/htslib/1.9+47-gc93b673/meta.yaml +++ b/recipes/htslib/1.9+47-gc93b673/meta.yaml @@ -26,13 +26,35 @@ source: features: - irods +requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - irods-dev >=4.1.12 + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libssl-dev + - libz-dev + run: + - libbz2 + - libcurl + - liblzma + - libssl + - libz + outputs: - - name: htslib + - name: htslib-bin version: {{ version }} requirements: build: - {{ compiler("c") }} - autoconf + - automake - make - perl host: @@ -62,7 +84,9 @@ outputs: build: - {{ compiler("c") }} - autoconf + - automake - make + - perl host: - irods-dev >=4.1.12 - libbz2-dev diff --git a/recipes/htslib/1.9+9-g6ec3b94/meta.yaml b/recipes/htslib/1.9+9-g6ec3b94/meta.yaml index f4512158..0cd77d34 100644 --- a/recipes/htslib/1.9+9-g6ec3b94/meta.yaml +++ b/recipes/htslib/1.9+9-g6ec3b94/meta.yaml @@ -26,13 +26,35 @@ source: features: - irods +requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - irods-dev >=4.1.12 + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libssl-dev + - libz-dev + run: + - libbz2 + - libcurl + - liblzma + - libssl + - libz + outputs: - - name: htslib + - name: htslib-bin version: {{ version }} requirements: build: - {{ compiler("c") }} - autoconf + - automake - make - perl host: @@ -62,7 +84,9 @@ outputs: build: - {{ compiler("c") }} - autoconf + - automake - make + - perl host: - irods-dev >=4.1.12 - libbz2-dev From 877ec673ddc466489b99b15ed7bef5692b206dca Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 7 Jan 2019 09:49:50 +0000 Subject: [PATCH 016/119] Added sub-package requirements to the package root requirements because conda-build does not pick them up from the sub-package definition. Renamed the samtools sub-package to samtools-bin because of https://github.com/conda/conda-build/issues/3313 --- recipes/samtools/1.9+2-g02d93a1/meta.yaml | 17 ++++++- recipes/samtools/1.9+37-g5708485/meta.yaml | 57 +++++++++++++++++++--- 2 files changed, 65 insertions(+), 9 deletions(-) diff --git a/recipes/samtools/1.9+2-g02d93a1/meta.yaml b/recipes/samtools/1.9+2-g02d93a1/meta.yaml index 1adca41e..ba882d99 100644 --- a/recipes/samtools/1.9+2-g02d93a1/meta.yaml +++ b/recipes/samtools/1.9+2-g02d93a1/meta.yaml @@ -17,13 +17,28 @@ source: git_url: https://github.com/samtools/samtools.git git_rev: 02d93a154a3c27f1acea6021e9e4d75898c2586c +requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - libhts-dev =={{ htslib_version }} + - libz-dev + run: + - libhts + - libz + outputs: - - name: samtools + - name: samtools-bin version: {{ version }} requirements: build: - {{ compiler("c") }} - autoconf + - automake - make - perl host: diff --git a/recipes/samtools/1.9+37-g5708485/meta.yaml b/recipes/samtools/1.9+37-g5708485/meta.yaml index 8af613a2..f6fb573b 100644 --- a/recipes/samtools/1.9+37-g5708485/meta.yaml +++ b/recipes/samtools/1.9+37-g5708485/meta.yaml @@ -11,7 +11,7 @@ about: summary: C library for high-throughput sequencing data formats. build: - number: 0 + number: 1 source: git_url: https://github.com/samtools/samtools.git @@ -19,12 +19,53 @@ source: requirements: build: - - gcc_npg >=7.3 - - htslib =={{ htslib_version }} - + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - libhts-dev =={{ htslib_version }} + - libz-dev run: - - htslib =={{ htslib_version }} + - libhts + - libz + +outputs: + - name: samtools-bin + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - libhts-dev =={{ htslib_version }} + - libz-dev + run: + - libhts + - libz + files: + - bin/ace2sam + - bin/maq2sam-* + - bin/md5* + - bin/plot-bamstats + - bin/samtools + - bin/wgsim + - bin/*.pl + - bin/*.py + test: + commands: + - echo '@HD VN:1.0 SO:coordinate' | samtools view -test: - commands: - - echo '@HD VN:1.0 SO:coordinate' | samtools view + - name: samtools-dev + version: {{ version }} + requirements: + run: + - libhts =={{ htslib_version }} + - libz + files: + - include/samtools/*.h + - lib/libbam.a From b39a6788e939a7f9e6cba28dfc5f01713cd8eb0b Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 7 Jan 2019 20:11:33 +0000 Subject: [PATCH 017/119] Added io_lib, updated to 1.14.11 and renamed from staden_io_lib. --- recipes/io_lib/1.14.11/build.sh | 11 +++ recipes/io_lib/1.14.11/meta.yaml | 153 +++++++++++++++++++++++++++++++ 2 files changed, 164 insertions(+) create mode 100755 recipes/io_lib/1.14.11/build.sh create mode 100644 recipes/io_lib/1.14.11/meta.yaml diff --git a/recipes/io_lib/1.14.11/build.sh b/recipes/io_lib/1.14.11/build.sh new file mode 100755 index 00000000..f5f91d65 --- /dev/null +++ b/recipes/io_lib/1.14.11/build.sh @@ -0,0 +1,11 @@ +#!/bin/sh + +set -ex + +n="$CPU_COUNT" + +./configure --prefix="$PREFIX" --with-zlib="$PREFIX" --with-libcurl="$PREFIX" + +make -j $n CPPFLAGS="-I$PREFIX/include" \ + LDFLAGS="-Wl,-rpath-link,$PREFIX/lib -Wl,--disable-new-dtags -L$PREFIX/lib" +make install prefix="$PREFIX" diff --git a/recipes/io_lib/1.14.11/meta.yaml b/recipes/io_lib/1.14.11/meta.yaml new file mode 100644 index 00000000..d7f4ac66 --- /dev/null +++ b/recipes/io_lib/1.14.11/meta.yaml @@ -0,0 +1,153 @@ +{% set version = "1.14.11" %} +{% set sha256 = "arse" %} + +package: + name: io_lib + version: "{{ version }}" + +about: + home: https://sourceforge.net/projects/staden + license: BSD + summary: DNA sequence assembly, editing and analysis tools. + +build: + number: 4 + +source: + url: https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-14-11/io_lib-{{ version }}.tar.gz + fn: io_lib-{{ version }}.tar.gz + sha256: {{ sha256 }} + +requirements: + build: + - {{ compiler("c") }} + - autoconf + host: + - irods-dev >=4.1.12 + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libz-dev + run: + - libbz2 + - libcurl + - liblzma + - libz + +outputs: + - name: io_lib-bin + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + host: + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libz-dev + run: + - {{ pin_subpackage("libstaden-read", exact=True) }} + - libbz2 + - libcurl + - liblzma + - libz + files: + - bin/append_sff + - bin/convert_trace + - bin/cram_dump + - bin/cram_filter + - bin/cram_index + - bin/cram_size + - bin/extract_fastq + - bin/extract_qual + - bin/extract_seq + - bin/get_comment + - bin/hash_exp + - bin/hash_extract + - bin/hash_list + - bin/hash_sff + - bin/hash_tar + - bin/index_tar + - bin/makeSCF + - bin/scf_dump + - bin/scf_info + - bin/scf_update + - bin/scram_flagstat + - bin/scram_merge + - bin/scram_pileup + - bin/scram_test + - bin/scramble + - bin/srf2fasta + - bin/srf2fastq + - bin/srf_dump_all + - bin/srf_extract_hash + - bin/srf_extract_linear + - bin/srf_filter + - bin/srf_index_hash + - bin/srf_info + - bin/srf_list + - bin/trace_dump + - bin/ztr_dump + - share/man/man1/scramble.1 + - share/man/man1/srf2fasta.1 + - share/man/man1/srf2fastq.1 + - share/man/man1/srf_index_hash.1 + - share/man/man1/srf_info.1 + - share/man/man1/srf_list.1 + test: + commands: + - scramble -h + + - name: libstaden-read + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + host: + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libz-dev + run: + - libbz2 + - libcurl + - liblzma + - libz + files: + - lib/libstaden-read* + test: + commands: + - test -f ${PREFIX}/lib/libstaden-read.a + - test -h ${PREFIX}/lib/libstaden-read.so + + - name: libstaden-read-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libstaden-read", exact=True) }} + files: + - bin/io_lib-config + - include/io_lib + - share/man/man3/ExperimentFile.3 + - share/man/man3/exp2read.3 + - share/man/man3/fread_reading.3 + - share/man/man3/fread_scf.3 + - share/man/man3/fwrite_reading.3 + - share/man/man3/fwrite_scf.3 + - share/man/man3/read2exp.3 + - share/man/man3/read2scf.3 + - share/man/man3/read_allocate.3 + - share/man/man3/read_deallocate.3 + - share/man/man3/read_reading.3 + - share/man/man3/read_scf.3 + - share/man/man3/read_scf_header.3 + - share/man/man3/scf2read.3 + - share/man/man3/write_reading.3 + - share/man/man3/write_scf.3 + - share/man/man3/write_scf_header.3 + - share/man/man4/Read.4 + test: + commands: + - test -f ${PREFIX}/include/io_lib/io_lib_config.h From 2bafd6e63262006a32257cfe3f6080de72bc7ebc Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 7 Jan 2019 20:11:33 +0000 Subject: [PATCH 018/119] Added io_lib, updated to 1.14.11 and renamed from staden_io_lib. --- recipes/io_lib/1.14.11/build.sh | 11 +++ recipes/io_lib/1.14.11/meta.yaml | 153 +++++++++++++++++++++++++++++++ 2 files changed, 164 insertions(+) create mode 100755 recipes/io_lib/1.14.11/build.sh create mode 100644 recipes/io_lib/1.14.11/meta.yaml diff --git a/recipes/io_lib/1.14.11/build.sh b/recipes/io_lib/1.14.11/build.sh new file mode 100755 index 00000000..f5f91d65 --- /dev/null +++ b/recipes/io_lib/1.14.11/build.sh @@ -0,0 +1,11 @@ +#!/bin/sh + +set -ex + +n="$CPU_COUNT" + +./configure --prefix="$PREFIX" --with-zlib="$PREFIX" --with-libcurl="$PREFIX" + +make -j $n CPPFLAGS="-I$PREFIX/include" \ + LDFLAGS="-Wl,-rpath-link,$PREFIX/lib -Wl,--disable-new-dtags -L$PREFIX/lib" +make install prefix="$PREFIX" diff --git a/recipes/io_lib/1.14.11/meta.yaml b/recipes/io_lib/1.14.11/meta.yaml new file mode 100644 index 00000000..6d688023 --- /dev/null +++ b/recipes/io_lib/1.14.11/meta.yaml @@ -0,0 +1,153 @@ +{% set version = "1.14.11" %} +{% set sha256 = "a172cb66416794fdd9c1fc443f722f7e3439b52c99510b9a60f828392b9989e4" %} + +package: + name: io_lib + version: "{{ version }}" + +about: + home: https://sourceforge.net/projects/staden + license: BSD + summary: DNA sequence assembly, editing and analysis tools. + +build: + number: 4 + +source: + url: https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-14-11/io_lib-{{ version }}.tar.gz + fn: io_lib-{{ version }}.tar.gz + sha256: {{ sha256 }} + +requirements: + build: + - {{ compiler("c") }} + - autoconf + host: + - irods-dev >=4.1.12 + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libz-dev + run: + - libbz2 + - libcurl + - liblzma + - libz + +outputs: + - name: io_lib-bin + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + host: + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libz-dev + run: + - {{ pin_subpackage("libstaden-read", exact=True) }} + - libbz2 + - libcurl + - liblzma + - libz + files: + - bin/append_sff + - bin/convert_trace + - bin/cram_dump + - bin/cram_filter + - bin/cram_index + - bin/cram_size + - bin/extract_fastq + - bin/extract_qual + - bin/extract_seq + - bin/get_comment + - bin/hash_exp + - bin/hash_extract + - bin/hash_list + - bin/hash_sff + - bin/hash_tar + - bin/index_tar + - bin/makeSCF + - bin/scf_dump + - bin/scf_info + - bin/scf_update + - bin/scram_flagstat + - bin/scram_merge + - bin/scram_pileup + - bin/scram_test + - bin/scramble + - bin/srf2fasta + - bin/srf2fastq + - bin/srf_dump_all + - bin/srf_extract_hash + - bin/srf_extract_linear + - bin/srf_filter + - bin/srf_index_hash + - bin/srf_info + - bin/srf_list + - bin/trace_dump + - bin/ztr_dump + - share/man/man1/scramble.1 + - share/man/man1/srf2fasta.1 + - share/man/man1/srf2fastq.1 + - share/man/man1/srf_index_hash.1 + - share/man/man1/srf_info.1 + - share/man/man1/srf_list.1 + test: + commands: + - scramble -h + + - name: libstaden-read + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + host: + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libz-dev + run: + - libbz2 + - libcurl + - liblzma + - libz + files: + - lib/libstaden-read* + test: + commands: + - test -f ${PREFIX}/lib/libstaden-read.a + - test -h ${PREFIX}/lib/libstaden-read.so + + - name: libstaden-read-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libstaden-read", exact=True) }} + files: + - bin/io_lib-config + - include/io_lib + - share/man/man3/ExperimentFile.3 + - share/man/man3/exp2read.3 + - share/man/man3/fread_reading.3 + - share/man/man3/fread_scf.3 + - share/man/man3/fwrite_reading.3 + - share/man/man3/fwrite_scf.3 + - share/man/man3/read2exp.3 + - share/man/man3/read2scf.3 + - share/man/man3/read_allocate.3 + - share/man/man3/read_deallocate.3 + - share/man/man3/read_reading.3 + - share/man/man3/read_scf.3 + - share/man/man3/read_scf_header.3 + - share/man/man3/scf2read.3 + - share/man/man3/write_reading.3 + - share/man/man3/write_scf.3 + - share/man/man3/write_scf_header.3 + - share/man/man4/Read.4 + test: + commands: + - test -f ${PREFIX}/include/io_lib/io_lib_config.h From fa727c048949ee89d232f3368e1e4e9a8ec86cc6 Mon Sep 17 00:00:00 2001 From: Keith James Date: Wed, 9 Jan 2019 08:47:22 +0000 Subject: [PATCH 019/119] Added sub-package requirements to the package root requirements because conda-build does not pick them up from the sub-package definition. Renamed the root package to libjansson-pkg because of https://github.com/conda/conda-build/issues/3313 --- recipes/jansson/2.1.0/meta.yaml | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/recipes/jansson/2.1.0/meta.yaml b/recipes/jansson/2.1.0/meta.yaml index 3a5e6438..627bd4a3 100644 --- a/recipes/jansson/2.1.0/meta.yaml +++ b/recipes/jansson/2.1.0/meta.yaml @@ -2,7 +2,7 @@ {% set sha256 = "b0a899f90ade82e42da0ecabc8af1fa296d69691e7c0786c4994fb79d4833ebb" %} package: - name: libjansson + name: libjansson-pkg version: "{{ version }}" about: @@ -18,6 +18,15 @@ source: build: number: 1 +requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - libtool + - make + - perl + outputs: - name: libjansson version: {{ version }} From f4b53f23a8d470caf3d525c3ad0644dd158162fe Mon Sep 17 00:00:00 2001 From: Keith James Date: Wed, 9 Jan 2019 08:48:46 +0000 Subject: [PATCH 020/119] Added sub-package requirements to the package root requirements because conda-build does not pick them up from the sub-package definition. Renamed the libgd package to libgd-pkg because of https://github.com/conda/conda-build/issues/3313 --- recipes/libgd/2.2.5/meta.yaml | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/recipes/libgd/2.2.5/meta.yaml b/recipes/libgd/2.2.5/meta.yaml index a85b9475..cf375ffc 100644 --- a/recipes/libgd/2.2.5/meta.yaml +++ b/recipes/libgd/2.2.5/meta.yaml @@ -2,7 +2,7 @@ {% set sha256 = "a66111c9b4a04e818e9e2a37d7ae8d4aae0939a100a36b0ffb52c706a09074b5" %} package: - name: libgd + name: libgd-pkg version: "{{ version }}" about: @@ -18,6 +18,18 @@ source: build: number: 1 +requirements: + build: + - {{ compiler("c") }} + - libtool + - pkg-config + host: + - libpng-dev + - libz-dev + run: + - libpng + - libz + outputs: - name: libgd-bin version: {{ version }} From 78df1f9217650046f778859f926daae0206a420e Mon Sep 17 00:00:00 2001 From: Keith James Date: Wed, 9 Jan 2019 08:50:19 +0000 Subject: [PATCH 021/119] Added sub-package requirements to the package root requirements because conda-build does not pick them up from the sub-package definition. Renamed the libpng package to libpng-pkg because of https://github.com/conda/conda-build/issues/3313 --- recipes/libpng/1.6.34/meta.yaml | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/recipes/libpng/1.6.34/meta.yaml b/recipes/libpng/1.6.34/meta.yaml index ed02d6a4..4ddd7b6f 100644 --- a/recipes/libpng/1.6.34/meta.yaml +++ b/recipes/libpng/1.6.34/meta.yaml @@ -2,7 +2,7 @@ {% set sha256 = "574623a4901a9969080ab4a2df9437026c8a87150dfd5c235e28c94b212964a7" %} package: - name: libpng + name: libpng-pkg version: "{{ version }}" about: @@ -18,6 +18,17 @@ source: build: number: 1 +requirements: + build: + - {{ compiler("c") }} + - libtool + - make + - pkg-config + host: + - libz-dev + run: + - libz + outputs: - name: libpng version: {{ version }} @@ -50,4 +61,3 @@ outputs: test: commands: - test -f ${PREFIX}/include/png.h - From 97b4a7c304693849ff69dd0bc88f94a77b81a653 Mon Sep 17 00:00:00 2001 From: Keith James Date: Wed, 9 Jan 2019 08:51:45 +0000 Subject: [PATCH 022/119] Added sub-package requirements to the package root requirements because conda-build does not pick them up from the sub-package definition. Renamed the pcre package to pcre-pkg because of https://github.com/conda/conda-build/issues/3313 --- recipes/pcre/8.41/meta.yaml | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/recipes/pcre/8.41/meta.yaml b/recipes/pcre/8.41/meta.yaml index d4272336..6145b19f 100644 --- a/recipes/pcre/8.41/meta.yaml +++ b/recipes/pcre/8.41/meta.yaml @@ -2,7 +2,7 @@ {% set sha256 = "244838e1f1d14f7e2fa7681b857b3a8566b74215f28133f14a8f5e59241b682c" %} package: - name: pcre + name: pcre-pkg version: "{{ version }}" about: @@ -18,6 +18,20 @@ source: fn: pcre-{{ version }}.tar.gz sha256: {{ sha256 }} +requirements: + build: + - {{ compiler("c") }} + - {{ compiler("cxx") }} + - make + host: + - libbz2-dev + - liblzma-dev + - libz-dev + run: + - libbz2 + - liblzma + - libz + outputs: - name: pcre version: {{ version }} From 14ace99338e4775abb402a115b3259d9d8355265 Mon Sep 17 00:00:00 2001 From: Keith James Date: Wed, 9 Jan 2019 08:53:26 +0000 Subject: [PATCH 023/119] Added sub-package requirements to the package root requirements because conda-build does not pick them up from the sub-package definition. Renamed the libxml2 package to libxml2-pkg because of https://github.com/conda/conda-build/issues/3313 --- recipes/libxml2/2.9.7/meta.yaml | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/recipes/libxml2/2.9.7/meta.yaml b/recipes/libxml2/2.9.7/meta.yaml index ab1c15da..65cae452 100644 --- a/recipes/libxml2/2.9.7/meta.yaml +++ b/recipes/libxml2/2.9.7/meta.yaml @@ -2,7 +2,7 @@ {% set sha256 = "f63c5e7d30362ed28b38bfa1ac6313f9a80230720b7fb6c80575eeab3ff5900c" %} package: - name: libxml2 + name: libxml2-pkg version: "{{ version }}" about: @@ -18,6 +18,17 @@ source: fn: libxml2-{{ version }}.tar.gz sha256: {{ sha256 }} +requirements: + build: + - {{ compiler("c") }} + - make + host: + - liblzma-dev + - libz-dev + run: + - liblzma + - libz + outputs: - name: libxml2-bin requirements: From a6f979ff6b4ca8d5e79f55fa931d92b1b7e745dd Mon Sep 17 00:00:00 2001 From: Keith James Date: Wed, 9 Jan 2019 08:54:29 +0000 Subject: [PATCH 024/119] Added sub-package requirements to the package root requirements because conda-build does not pick them up from the sub-package definition. Renamed the libxslt package to libxslt-pkg because of https://github.com/conda/conda-build/issues/3313 --- recipes/libxslt/1.1.32/meta.yaml | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/recipes/libxslt/1.1.32/meta.yaml b/recipes/libxslt/1.1.32/meta.yaml index ba35bd0a..cefe39e7 100644 --- a/recipes/libxslt/1.1.32/meta.yaml +++ b/recipes/libxslt/1.1.32/meta.yaml @@ -2,7 +2,7 @@ {% set sha256 = "526ecd0abaf4a7789041622c3950c0e7f2c4c8835471515fd77eec684a355460" %} package: - name: libxslt + name: libxslt-pkg version: "{{ version }}" about: @@ -12,12 +12,25 @@ about: build: number: 1 - + source: url: ftp://xmlsoft.org/libxslt/libxslt-{{ version }}.tar.gz fn: libxslt-{{ version }}.tar.gz sha256: {{ sha256 }} +requirements: + build: + - {{ compiler("c") }} + - make + host: + - liblzma-dev + - libxml2-dev + - libz-dev + run: + - liblzma + - libxml2 + - libz + outputs: - name: libxslt-bin version: {{ version }} From 88de8750123e9925f99a9698c3afa58e62cb15ba Mon Sep 17 00:00:00 2001 From: Keith James Date: Wed, 9 Jan 2019 08:56:41 +0000 Subject: [PATCH 025/119] Added sub-package requirements to the package root requirements because conda-build does not pick them up from the sub-package definition. Renamed the libmaus2 package to libmaus2-pkg because of https://github.com/conda/conda-build/issues/3313 --- recipes/libmaus2/2.0.420/meta.yaml | 19 ++++++++++++++++++- 1 file changed, 18 insertions(+), 1 deletion(-) diff --git a/recipes/libmaus2/2.0.420/meta.yaml b/recipes/libmaus2/2.0.420/meta.yaml index 87453aa3..176689c1 100644 --- a/recipes/libmaus2/2.0.420/meta.yaml +++ b/recipes/libmaus2/2.0.420/meta.yaml @@ -2,7 +2,7 @@ {% set sha256 = "0d28932e363e80b4519b04a512df899189c612a4c097130219d6e0ebbfde2a34" %} package: - name: libmaus2 + name: libmaus2-pkg version: "{{ version }}" about: @@ -18,6 +18,23 @@ source: fn: libmaus2-{{ version }}.tar.gz sha256: {{ sha256 }} +requirements: + build: + - {{ compiler("cxx") }} + - make + - pkg-config + host: + - irods-dev + - libgnutls-dev + - libnettle-dev + - libstaden-read-dev + - libz-dev + run: + - libgnutls + - libnettle + - libstaden-read + - libz + outputs: - name: libmaus2 version: {{ version }} From f4bfc92ffb09ff42d0f1ce85fcd28a0787cb28fd Mon Sep 17 00:00:00 2001 From: Keith James Date: Wed, 9 Jan 2019 15:35:33 +0000 Subject: [PATCH 026/119] Removed the npg_qc_utils directory (we no longer download into this, so it doesn't exist) --- recipes/npg_qc_utils/65.0/build.sh | 3 --- 1 file changed, 3 deletions(-) diff --git a/recipes/npg_qc_utils/65.0/build.sh b/recipes/npg_qc_utils/65.0/build.sh index c57e7461..4131e1d4 100755 --- a/recipes/npg_qc_utils/65.0/build.sh +++ b/recipes/npg_qc_utils/65.0/build.sh @@ -4,8 +4,6 @@ set -ex n="$CPU_COUNT" -pushd npg_qc_utils - pushd fastq_summ mkdir -p build make -j $n CC="$GCC" \ @@ -40,4 +38,3 @@ make -j $n CC="$GCC" \ make install installdir="$PREFIX/bin" popd -popd From ead0b2cb1f1526f8bacf1a72b4fdc94c674b856f Mon Sep 17 00:00:00 2001 From: Keith James Date: Wed, 9 Jan 2019 15:36:44 +0000 Subject: [PATCH 027/119] Added a missing build dependency on automake. --- recipes/tears/1.2.4/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/tears/1.2.4/meta.yaml b/recipes/tears/1.2.4/meta.yaml index f423b707..64202c50 100644 --- a/recipes/tears/1.2.4/meta.yaml +++ b/recipes/tears/1.2.4/meta.yaml @@ -20,6 +20,7 @@ requirements: build: - {{ compiler("c") }} - autoconf + - automake - make - perl host: From 7ce92fcee15623f5233376b93c0b94de32412970 Mon Sep 17 00:00:00 2001 From: Keith James Date: Wed, 9 Jan 2019 15:37:44 +0000 Subject: [PATCH 028/119] Added missing build operations and tests for creating the samtools-dev sub-package. Pinned the runtime version of htslib to the build version. --- recipes/samtools/1.9+2-g02d93a1/meta.yaml | 8 ++++++-- recipes/samtools/1.9+37-g5708485/meta.yaml | 8 ++++++-- 2 files changed, 12 insertions(+), 4 deletions(-) diff --git a/recipes/samtools/1.9+2-g02d93a1/meta.yaml b/recipes/samtools/1.9+2-g02d93a1/meta.yaml index ba882d99..2f87c7da 100644 --- a/recipes/samtools/1.9+2-g02d93a1/meta.yaml +++ b/recipes/samtools/1.9+2-g02d93a1/meta.yaml @@ -28,7 +28,7 @@ requirements: - libhts-dev =={{ htslib_version }} - libz-dev run: - - libhts + - libhts =={{ htslib_version }} - libz outputs: @@ -45,7 +45,7 @@ outputs: - libhts-dev =={{ htslib_version }} - libz-dev run: - - libhts + - libhts =={{ htslib_version }} - libz files: - bin/ace2sam @@ -69,3 +69,7 @@ outputs: files: - include/samtools/*.h - lib/libbam.a + test: + commands: + - test -f ${PREFIX}/include/samtools/sam.h + - test -f ${PREFIX}/lib/libbam.a diff --git a/recipes/samtools/1.9+37-g5708485/meta.yaml b/recipes/samtools/1.9+37-g5708485/meta.yaml index f6fb573b..2e5719cd 100644 --- a/recipes/samtools/1.9+37-g5708485/meta.yaml +++ b/recipes/samtools/1.9+37-g5708485/meta.yaml @@ -28,7 +28,7 @@ requirements: - libhts-dev =={{ htslib_version }} - libz-dev run: - - libhts + - libhts =={{ htslib_version }} - libz outputs: @@ -45,7 +45,7 @@ outputs: - libhts-dev =={{ htslib_version }} - libz-dev run: - - libhts + - libhts =={{ htslib_version }} - libz files: - bin/ace2sam @@ -69,3 +69,7 @@ outputs: files: - include/samtools/*.h - lib/libbam.a + test: + commands: + - test -f ${PREFIX}/include/samtools/sam.h + - test -f ${PREFIX}/lib/libbam.a From cb3303ccfdf617337afda167a8429af0ceef4d93 Mon Sep 17 00:00:00 2001 From: Keith James Date: Wed, 9 Jan 2019 15:47:37 +0000 Subject: [PATCH 029/119] Added missing libexslt library to the package. --- recipes/libxslt/1.1.32/meta.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/recipes/libxslt/1.1.32/meta.yaml b/recipes/libxslt/1.1.32/meta.yaml index cefe39e7..7917a1bc 100644 --- a/recipes/libxslt/1.1.32/meta.yaml +++ b/recipes/libxslt/1.1.32/meta.yaml @@ -69,10 +69,13 @@ outputs: - libz files: - lib/libxslt.* + - lib/libexslt.* test: commands: - test -f ${PREFIX}/lib/libxslt.a - test -h ${PREFIX}/lib/libxslt.so + - test -f ${PREFIX}/lib/libexslt.a + - test -h ${PREFIX}/lib/libexslt.so - name: libxslt-dev version: {{ version }} From fe0e210b0acf0e1a945868324a2f196dc8109ab4 Mon Sep 17 00:00:00 2001 From: Keith James Date: Fri, 11 Jan 2019 16:09:14 +0000 Subject: [PATCH 030/119] Avoid using a specific CentOS version when globbing for files. --- recipes/irods/4.1.12/build.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/irods/4.1.12/build.sh b/recipes/irods/4.1.12/build.sh index d848a9c1..c3478c0a 100644 --- a/recipes/irods/4.1.12/build.sh +++ b/recipes/irods/4.1.12/build.sh @@ -93,8 +93,8 @@ if [ -f /etc/redhat-release ]; then cd build - unrpm_data irods-icommands-4.1.12-64bit-centos5.rpm - unrpm_data irods-dev-4.1.12-64bit-centos5.rpm + unrpm_data irods-icommands-4.1.12-64bit-centos[0-9].rpm + unrpm_data irods-dev-4.1.12-64bit-centos[0-9].rpm fi # Fix all the absolute symlinks pointing to /usr/include From 6cea479ea06d328fb43b88ff115f45fe52487c15 Mon Sep 17 00:00:00 2001 From: Keith James Date: Fri, 11 Jan 2019 16:52:24 +0000 Subject: [PATCH 031/119] Fixes missing include path discovered while building on CentOS 7. --- recipes/blat/35/build.sh | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/blat/35/build.sh b/recipes/blat/35/build.sh index 8e0eef53..e51eb3e5 100755 --- a/recipes/blat/35/build.sh +++ b/recipes/blat/35/build.sh @@ -5,6 +5,8 @@ set -ex n="$CPU_COUNT" mkdir -p "$SRC_DIR/bin" + +export XINC="-I$PREFIX/include" make -j $n MACHTYPE=X86_64 BINDIR="$SRC_DIR/bin" \ CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" From 9aee69a4b6c12114f2af18d2194dabced894c120 Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 14 Jan 2019 10:16:27 +0000 Subject: [PATCH 032/119] Use this Makefile's non-standard way of setting an include path. This bug was masked previously because a compatible zlib header was picked up from the default search path. --- recipes/verifybamid/1.1.3/build.sh | 2 ++ recipes/verifybamid/1.1.3/meta.yaml | 2 ++ recipes/verifybamid/1.1.3/verifybamid.patch | 13 +++++++++++++ 3 files changed, 17 insertions(+) create mode 100644 recipes/verifybamid/1.1.3/verifybamid.patch diff --git a/recipes/verifybamid/1.1.3/build.sh b/recipes/verifybamid/1.1.3/build.sh index fdf573a9..31bbf91b 100755 --- a/recipes/verifybamid/1.1.3/build.sh +++ b/recipes/verifybamid/1.1.3/build.sh @@ -4,6 +4,8 @@ set -ex n="$CPU_COUNT" +export USER_INCLUDES="-I$PREFIX/include" + cd libStatGen make -j $n CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" diff --git a/recipes/verifybamid/1.1.3/meta.yaml b/recipes/verifybamid/1.1.3/meta.yaml index 23e282b1..2f2cc9b7 100644 --- a/recipes/verifybamid/1.1.3/meta.yaml +++ b/recipes/verifybamid/1.1.3/meta.yaml @@ -17,6 +17,8 @@ source: - git_url: https://github.com/statgen/verifyBamID.git git_rev: v{{ version }} folder: verifybamid + patches: + - verifybamid.patch - git_url: https://github.com/statgen/libStatGen.git git_rev: v{{ libstatgen_version }} folder: libStatGen diff --git a/recipes/verifybamid/1.1.3/verifybamid.patch b/recipes/verifybamid/1.1.3/verifybamid.patch new file mode 100644 index 00000000..3c15518d --- /dev/null +++ b/recipes/verifybamid/1.1.3/verifybamid.patch @@ -0,0 +1,13 @@ +diff --git src/Makefile src/Makefile +index 017bcc2..a2a5df5 100644 +--- src/Makefile ++++ src/Makefile +@@ -26,7 +26,7 @@ HDRONLY = + USER_COMPILE_VARS = + + # Specify any additional includes you need. +-USER_INCLUDES = -I. ++USER_INCLUDES ?= -I. + + # Specify any additional warnings you need to enable. + # Example: From e51ff165f60253a3459b7074de1d06307dd431a0 Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 14 Jan 2019 11:10:34 +0000 Subject: [PATCH 033/119] Ensure that the correct headers are picked up i.e. baton's dependencies rather than iRODS' version of the same dependencies. --- recipes/baton/1.1.0/build.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/baton/1.1.0/build.sh b/recipes/baton/1.1.0/build.sh index d48ce4b2..db65188a 100755 --- a/recipes/baton/1.1.0/build.sh +++ b/recipes/baton/1.1.0/build.sh @@ -5,9 +5,9 @@ set -ex n="$CPU_COUNT" ./configure --prefix="$PREFIX" --with-irods="$PREFIX" \ - CPPFLAGS="-I$PREFIX/include/irods" \ + CPPFLAGS="-I$PREFIX/include -I$PREFIX/include/irods" \ LDFLAGS="-L$PREFIX/lib -L$PREFIX/lib/irods/externals" -make -j $n CPPFLAGS="-I$PREFIX/include/irods" \ +make -j $n CPPFLAGS="-I$PREFIX/include -I$PREFIX/include/irods" \ LDFLAGS="-L$PREFIX/lib -L$PREFIX/lib/irods/externals" make install prefix="$PREFIX" From feb2ef2c15b8d5d29a973b2893949304d1bf9ded Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 14 Jan 2019 11:34:03 +0000 Subject: [PATCH 034/119] Ensure CPPFLAGS and LDFLAGS set for configure. --- recipes/libxml2/2.9.7/build.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/libxml2/2.9.7/build.sh b/recipes/libxml2/2.9.7/build.sh index 6bd4ca82..02fffc2b 100644 --- a/recipes/libxml2/2.9.7/build.sh +++ b/recipes/libxml2/2.9.7/build.sh @@ -4,7 +4,8 @@ set -ex n="$CPU_COUNT" -./configure prefix="$PREFIX" --without-python +CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" \ + ./configure prefix="$PREFIX" --without-python make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install From 4f881098042c37c0a6ac8763a92d08a2e6d854bc Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 14 Jan 2019 11:45:59 +0000 Subject: [PATCH 035/119] Avoid building Python support. --- recipes/libxslt/1.1.32/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/libxslt/1.1.32/build.sh b/recipes/libxslt/1.1.32/build.sh index 46c7ff8d..6bd4ca82 100644 --- a/recipes/libxslt/1.1.32/build.sh +++ b/recipes/libxslt/1.1.32/build.sh @@ -4,7 +4,7 @@ set -ex n="$CPU_COUNT" -./configure prefix="$PREFIX" +./configure prefix="$PREFIX" --without-python make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install From 2daeef14f11eec3471f3b68d737cd3a21a5458b1 Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 14 Jan 2019 12:27:45 +0000 Subject: [PATCH 036/119] Avoid building docs. Building docs has the side-effect of building the example code, which has a Makefile that does not respect Conda's $LD environment variable to set the linker. As a consequence, the build may use a system linker (/usr/bin/ld), resulting in errors if that is an unsuitable version. --- recipes/gnutls/3.4.17/build.sh | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/gnutls/3.4.17/build.sh b/recipes/gnutls/3.4.17/build.sh index 54dae1db..c5b54c48 100644 --- a/recipes/gnutls/3.4.17/build.sh +++ b/recipes/gnutls/3.4.17/build.sh @@ -9,9 +9,10 @@ n="$CPU_COUNT" --with-libz-prefix="$PREFIX" \ --without-idn \ --without-p11-kit \ - --without-tpm + --without-tpm \ + --disable-doc -make -j $n prefix="$PREFIX" CC="$GCC" \ +make -j $n prefix="$PREFIX" CC="$GCC" LD="$LD" \ CPPFLAGS="-I$PREFIX/include" \ LDFLAGS="-Wl,-rpath-link,$PREFIX/lib -Wl,--disable-new-dtags" make install prefix="$PREFIX" From 596b7da17d6173b01cb64dded8f43531153eedb2 Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 14 Jan 2019 13:43:52 +0000 Subject: [PATCH 037/119] Copy headers for samtools library. Ensure CPPFLAGS and LDFLAGS are set during the build. --- recipes/samtools/1.9+37-g5708485/build.sh | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/samtools/1.9+37-g5708485/build.sh b/recipes/samtools/1.9+37-g5708485/build.sh index 70c84b14..fe272db9 100755 --- a/recipes/samtools/1.9+37-g5708485/build.sh +++ b/recipes/samtools/1.9+37-g5708485/build.sh @@ -1,8 +1,8 @@ #!/bin/sh -set -e +set -ex -n=`expr $CPU_COUNT / 4 \| 1` +n="$CPU_COUNT" autoreconf ./configure --prefix="$PREFIX" \ @@ -10,5 +10,9 @@ autoreconf --without-curses \ CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make -j $n +make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install prefix="$PREFIX" + +mkdir p "$PREFIX/include/samtools" +cp "$SRC_DIR/"*.h "$PREFIX/include/samtools/" +cp "$SRC_DIR/libbam.a" "$PREFIX/lib" From 2e33412ce67648f86003f73534b4ff3dc2f8a4c7 Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 14 Jan 2019 13:51:04 +0000 Subject: [PATCH 038/119] Ensure CPPFLAGS and LDFLAGS set for configure. --- recipes/bcftools/1.9/build.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/bcftools/1.9/build.sh b/recipes/bcftools/1.9/build.sh index 25565d17..41ef0f38 100644 --- a/recipes/bcftools/1.9/build.sh +++ b/recipes/bcftools/1.9/build.sh @@ -4,7 +4,8 @@ set -ex n="$CPU_COUNT" -./configure --prefix="$PREFIX" --with-htslib="$PREFIX" +CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" \ + ./configure --prefix="$PREFIX" --with-htslib="$PREFIX" make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install prefix="$PREFIX" From 59db358db81c1587e17dab51156520c73f8af814 Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 14 Jan 2019 17:16:46 +0000 Subject: [PATCH 039/119] Ensure that the correct (Conda) linker is used. --- recipes/freebayes/1.2.0/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/freebayes/1.2.0/build.sh b/recipes/freebayes/1.2.0/build.sh index 4bc047ac..d27f1446 100755 --- a/recipes/freebayes/1.2.0/build.sh +++ b/recipes/freebayes/1.2.0/build.sh @@ -2,7 +2,7 @@ set -ex -make -j 1 CC="$GCC" CXX="$CXX" \ +make -j 1 CC="$GCC" CXX="$CXX" LD="$LD" \ CXXFLAGS="-I$PREFIX/include" \ CPPFLAGS="-I$PREFIX/include" \ LDFLAGS="-L$PREFIX/lib" From e0a5ff91584dea1502dd4d17e9f8ee70673980c0 Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 15 Jan 2019 09:38:14 +0000 Subject: [PATCH 040/119] Patch bambi to build against the htslib shared library, rather than static. (NB. This patch is the reason bambi will report its version as 0.11.1-dirty) --- recipes/bambi/0.11.1/ax_with_htslib.patch | 12 ++++++++++++ recipes/bambi/0.11.1/build.sh | 4 ++-- recipes/bambi/0.11.1/meta.yaml | 9 ++++++--- 3 files changed, 20 insertions(+), 5 deletions(-) create mode 100644 recipes/bambi/0.11.1/ax_with_htslib.patch diff --git a/recipes/bambi/0.11.1/ax_with_htslib.patch b/recipes/bambi/0.11.1/ax_with_htslib.patch new file mode 100644 index 00000000..6e747ee6 --- /dev/null +++ b/recipes/bambi/0.11.1/ax_with_htslib.patch @@ -0,0 +1,12 @@ +index 40e8f48..1b8bafc 100644 +--- m4/ax_with_htslib.m4 ++++ m4/ax_with_htslib.m4 +@@ -71,7 +71,7 @@ AC_DEFUN([AX_WITH_HTSLIB], [ + LDFLAGS="-L$HTSLIB_HOME/lib $LDFLAGS" + ]) + +- LIBS="$HTSLIB_HOME/lib/libhts.a -lz -ldl -lbz2 -llzma -lpthread -lcurl -lcrypto" ++ LIBS="-lhts -lz -ldl -lbz2 -llzma -lpthread -lcurl -lcrypto" + + AC_MSG_CHECKING([checking htslib version]) + AC_RUN_IFELSE([AC_LANG_PROGRAM([ diff --git a/recipes/bambi/0.11.1/build.sh b/recipes/bambi/0.11.1/build.sh index c0e38156..0deb559a 100755 --- a/recipes/bambi/0.11.1/build.sh +++ b/recipes/bambi/0.11.1/build.sh @@ -6,8 +6,8 @@ autoreconf -fi n="$CPU_COUNT" -./configure --prefix="$PREFIX" --with-htslib="$PREFIX" \ - CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +CPPFLAGS="-I$PREFIX/include" LDFLAGS="-Wl,-rpath,$PREFIX/lib -L$PREFIX/lib" \ + ./configure --prefix="$PREFIX" --with-htslib="$PREFIX" make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install prefix="$PREFIX" diff --git a/recipes/bambi/0.11.1/meta.yaml b/recipes/bambi/0.11.1/meta.yaml index 065de0f6..e6650539 100644 --- a/recipes/bambi/0.11.1/meta.yaml +++ b/recipes/bambi/0.11.1/meta.yaml @@ -1,4 +1,5 @@ {% set version = "0.11.1" %} +{% set min_hts_version = "1.3.1" %} package: name: bambi @@ -10,11 +11,13 @@ about: summary: "A set of programs to manipulate SAM/BAM/CRAM files, using HTSLIB." build: - number: 3 + number: 4 source: git_url: https://github.com/wtsi-npg/bambi.git git_rev: 0.11.1 + patches: + - ax_with_htslib.patch requirements: build: @@ -26,12 +29,12 @@ requirements: - pkg-config host: - libgd-dev - - libhts-dev + - libhts-dev >={{ min_hts_version }} - libxml2-dev - libz-dev run: - libgd - - libhts + - libhts >={{ min_hts_version }} - libxml2 - libz From f84427c9cb5b26244ce248b392e61bff26326ea7 Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 15 Jan 2019 10:03:28 +0000 Subject: [PATCH 041/119] Added another patch to freebayes dependencies to make sure they respect $AR and $LD settinngthe desired archiver and linker. --- recipes/freebayes/1.2.0/meta.yaml | 1 + .../1.2.0/vcflib_smithwaterman_Makefile.patch | 16 ++++++++++++++++ 2 files changed, 17 insertions(+) create mode 100644 recipes/freebayes/1.2.0/vcflib_smithwaterman_Makefile.patch diff --git a/recipes/freebayes/1.2.0/meta.yaml b/recipes/freebayes/1.2.0/meta.yaml index 4d1be319..9f578e5b 100644 --- a/recipes/freebayes/1.2.0/meta.yaml +++ b/recipes/freebayes/1.2.0/meta.yaml @@ -21,6 +21,7 @@ source: - SeqLib_bwa_Makefile.patch - SeqLib_fermi-lite_Makefile.patch - vcflib_Makefile.patch + - vcflib_smithwaterman_Makefile.patch - vcflib_tabixpp_Makefile.patch - vcflib_tabixpp_htslib_Makefile.patch diff --git a/recipes/freebayes/1.2.0/vcflib_smithwaterman_Makefile.patch b/recipes/freebayes/1.2.0/vcflib_smithwaterman_Makefile.patch new file mode 100644 index 00000000..67c12bd1 --- /dev/null +++ b/recipes/freebayes/1.2.0/vcflib_smithwaterman_Makefile.patch @@ -0,0 +1,16 @@ +index 37bfc67..465b7e7 100644 +--- vcflib/smithwaterman/Makefile ++++ vcflib/smithwaterman/Makefile +@@ -25,10 +25,10 @@ all: $(EXE) sw.o + .PHONY: all + + libsw.a: smithwaterman.o BandedSmithWaterman.o SmithWatermanGotoh.o LeftAlign.o Repeats.o IndelAllele.o disorder.o +- ar rs $@ smithwaterman.o d SmithWatermanGotoh.o disorder.o BandedSmithWaterman.o LeftAlign.o Repeats.o IndelAllele.o ++ $(AR) rs $@ smithwaterman.o d SmithWatermanGotoh.o disorder.o BandedSmithWaterman.o LeftAlign.o Repeats.o IndelAllele.o + + sw.o: BandedSmithWaterman.o SmithWatermanGotoh.o LeftAlign.o Repeats.o IndelAllele.o disorder.o +- ld -r $^ -o sw.o -L. ++ $(LD) -r $^ -o sw.o -L. + #$(CXX) $(CFLAGS) -c -o smithwaterman.cpp $(OBJECTS_NO_MAIN) -I. + + ### @$(CXX) $(LDFLAGS) $(CFLAGS) -o $@ $^ -I. From 60fd3be806b50f14966136e5ff77e106c38028bc Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 15 Jan 2019 10:25:45 +0000 Subject: [PATCH 042/119] Added a build config to set CFLAGS for portable packages. --- config/conda_build_config.yaml | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 config/conda_build_config.yaml diff --git a/config/conda_build_config.yaml b/config/conda_build_config.yaml new file mode 100644 index 00000000..1c80fb22 --- /dev/null +++ b/config/conda_build_config.yaml @@ -0,0 +1,10 @@ +# This is the default build config which uses -march=x86-64 to create +# programs that are portable across all of our CPU architectures. +# Replacing this with e.g. -march=native will use instructions that +# may not be poratble to other types of machine. See +# https://gcc.gnu.org/onlinedocs/gcc/x86-Options.html#index-march-13 + +CFLAGS: >- + -march=x86-64 -mtune=generic + -fPIC -O2 + -ftree-vectorize -fstack-protector-strong -ffunction-sections -pipe From cebc2929e18b979301965eede416e86f9c6f3ba0 Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 15 Jan 2019 14:05:21 +0000 Subject: [PATCH 043/119] Depend on samtools-bin, rather than samtools. --- recipes/goleft/0.2.0/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/goleft/0.2.0/meta.yaml b/recipes/goleft/0.2.0/meta.yaml index 555b5243..2f272e59 100644 --- a/recipes/goleft/0.2.0/meta.yaml +++ b/recipes/goleft/0.2.0/meta.yaml @@ -11,7 +11,7 @@ about: summary: "goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary." build: - number: 0 + number: 1 binary_relocation: false source: @@ -20,7 +20,7 @@ source: requirements: run: - - samtools + - samtools-bin test: commands: From 00bce144b0aa4f37b163859fa93f5df52228fcb3 Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 28 Jan 2019 10:21:37 +0000 Subject: [PATCH 044/119] Fix gcc version to ensure building on all versions of Ubuntu that we use. Corrected the libtool package name. --- recipes/irods/4.1.12/build.sh | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/recipes/irods/4.1.12/build.sh b/recipes/irods/4.1.12/build.sh index c3478c0a..0f06b0c9 100644 --- a/recipes/irods/4.1.12/build.sh +++ b/recipes/irods/4.1.12/build.sh @@ -24,17 +24,22 @@ unrpm_data() { } install_gcc_ubuntu() { - sudo apt-get install -y g++ g++-4.8 gcc gcc-4.8 + GCC_VERSION= + grep precise /etc/lsb-release && GCC_VERSION="4.6" + grep xenial /etc/lsb-release && GCC_VERSION="4.8" + grep bionic /etc/lsb-release && GCC_VERSION="4.8" - sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 100 - sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 100 - sudo update-alternatives --set gcc /usr/bin/gcc-4.8 - sudo update-alternatives --set g++ /usr/bin/g++-4.8 + sudo apt-get install -y "g++-$GCC_VERSION" "gcc-$GCC_VERSION" + + sudo update-alternatives --install /usr/bin/gcc gcc "/usr/bin/gcc-$GCC_VERSION" 100 + sudo update-alternatives --install /usr/bin/g++ g++ "/usr/bin/g++-$GCC_VERSION" 100 + sudo update-alternatives --set gcc "/usr/bin/gcc-$GCC_VERSION" + sudo update-alternatives --set g++ "/usr/bin/g++-$GCC_VERSION" } install_deps_ubuntu() { sudo apt-get install -y autoconf automake help2man make \ - libtool-bin pkg-config texinfo + libtool pkg-config texinfo sudo apt-get install -y libjson-perl python-dev From 23d9a0c80f744f0886b716f3f8fd72f825a80d39 Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 29 Jan 2019 09:26:25 +0000 Subject: [PATCH 045/119] Added a record of the recipe file path so that the recipe may be found by its content, without recourse to directory naming conventions. --- scripts/package_sort.py | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/scripts/package_sort.py b/scripts/package_sort.py index 4292704a..224f1d23 100755 --- a/scripts/package_sort.py +++ b/scripts/package_sort.py @@ -1,6 +1,6 @@ #!/usr/bin/env python3 # -# Copyright © 2018 Genome Research Ltd. All rights reserved. +# Copyright © 2018, 2019 Genome Research Ltd. All rights reserved. # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -164,6 +164,11 @@ def add_listval(dikt, key, value): else: dikt[key] = [value] + # This dict maps a (package name, version Specifier) to the recipe + # file that defined it. It is used to determine which recipe to + # use to build a package. + pkg_recipes = {} + # This dict contains lists of Versions of package. # # Key: package name @@ -199,6 +204,8 @@ def add_listval(dikt, key, value): add_listval(pkg_versions, pkg_name, pkg_version) log.debug("package name: %s %s", pkg_name, pkg_version) + pkg_recipes[(pkg_name, pkg_version)] = recipe_file + pkg_reqs = [] base_reqs = recipe.get("requirements", {}) pkg_reqs += base_reqs.get("host", []) @@ -222,7 +229,7 @@ def add_listval(dikt, key, value): add_listval(pkg_requirements, (pkg_name, pkg_version), (req, spec)) - return pkg_versions, pkg_requirements, pkg_outputs + return pkg_recipes, pkg_versions, pkg_requirements, pkg_outputs def build_dependency_graph(graph, root_node, @@ -308,7 +315,7 @@ def build_dependency_graph(graph, root_node, type=str, nargs="?", default=".") parser.add_argument("-p", "--package", type=str, - help="Report dependentss (i.e. descendants) of the" + help="Report dependents (i.e. descendants) of the" "specified package") parser.add_argument("-v", "--version", type=str, help="Report dependents (i.e. descendants) of the" @@ -332,7 +339,7 @@ def build_dependency_graph(graph, root_node, base = args.recipes -pkg_versions, pkg_requirements, pkg_outputs = load_recipes(base) +pkg_recipes, pkg_versions, pkg_requirements, pkg_outputs = load_recipes(base) root_node="root" graph = nx.DiGraph(directed=True) @@ -350,4 +357,5 @@ def build_dependency_graph(graph, root_node, else: for node in nx.topological_sort(graph): if node is not root_node: - print(node[0], node[1]) + recipe = pkg_recipes[node] + print(node[0], node[1], os.path.dirname(recipe)) From 7e2c6b34c5401b7810aa842cd1c8e0e6758baabf Mon Sep 17 00:00:00 2001 From: Keith James Date: Thu, 7 Feb 2019 14:58:48 +0000 Subject: [PATCH 046/119] Added a --changes CLI option. This allows a user to specify a git branch against which to compare recipes. Only changed recipes and their ancestors will be reported. Used a formatter_class to preserve help formatting. --- scripts/package_sort.py | 110 ++++++++++++++++++++++++++++++++-------- 1 file changed, 88 insertions(+), 22 deletions(-) diff --git a/scripts/package_sort.py b/scripts/package_sort.py index 224f1d23..dd0eddd6 100755 --- a/scripts/package_sort.py +++ b/scripts/package_sort.py @@ -27,6 +27,7 @@ import argparse import functools import os +import subprocess import sys import yaml @@ -76,11 +77,39 @@ def find_recipe_files(dir): recipe_files = [] for dir, _, files in os.walk(base): for file in files: - if file == 'meta.yaml': + if file == "meta.yaml": recipe_files.append(os.path.join(dir, file)) return recipe_files +def find_changed_recipe_files(dir, branch="master"): + """ + Return the paths of Conda recipe meta.yaml files where something in + the recipe directory has changed relative to another git branch. + + :param dir str: The directory to search. + + :param branch str: The git branch to compare with. + + :returns: Paths of recipe files. + + :rtype: list str + """ + proc = subprocess.Popen(["git", "diff", "--name-only", + "--diff-filter=d", branch, dir], + stdout=subprocess.PIPE) + files = [line.rstrip().decode("utf-8") for line in proc.stdout] + dirs = list(set([os.path.dirname(f) for f in files])) + dirs.sort() + + recipe_files = [] + for dir in dirs: + recipe = os.path.join(dir, "meta.yaml") + if (os.path.isfile(recipe)): + recipe_files.append(recipe) + return recipe_files + + def make_template_env(recipe_files): """ Make a new Jinjer2 template environment by loading Conda recipes @@ -153,8 +182,7 @@ def find_package_version(req_pkg, pkg_index, spec=None): return list(spec.filter(candidates)) if spec else candidates -def load_recipes(dir): - recipe_files = find_recipe_files(base) +def load_recipes(recipe_files): template_env = make_template_env(recipe_files) # Append to a dict list value @@ -277,49 +305,69 @@ def build_dependency_graph(graph, root_node, "%s %s of candidates %s", parent_pkg, v, pkg_versions[parent_pkg]) else: - log.warn("Can't find required package %s", req_pkg) + log.warning("Can't find required package %s", + req_pkg) else: log.debug("%s has no requirements", ptup) graph.add_edge(ptup, root_node) return graph +def is_root_node(node): + return node == "root" + + +def print_node(node, pkg_recipes): + if not is_root_node(node): + recipe = pkg_recipes[node] + print(node[0], node[1], os.path.dirname(recipe)) + description = """ Reads Conda package recipe meta.yaml files under the specified directory (recursively) and reports package dependency information. -If no package is specified, a directed, acyclic graph of the -inter-package dependencies is calculated, and a topological sort of -that graph is printed to STDOUT. The utility of this is that it -describes an order in which to build packages whereby a later package -will only depend on previously built packages, never on package yet to -be built. This feature is essential because conda-build is no longer -capable of recursive from-source builds [1]. - -If a package and version are specified, a directed, acyclic graph of -the inter-package dependencies of its ancestors is calculated, and a +If no package is specified (with --package ), a +directed, acyclic graph of the inter-package dependencies is +calculated, and a topological sort of that graph is printed to +STDOUT. This information describes an order in which to build packages +whereby a later package will only depend on previously built packages, +never on package yet to be built. This feature is essential because +conda-build is no longer capable of recursive from-source builds [1]. + +If a package and version are specified (with --package +and --version ), a directed, acyclic graph of the +inter-package dependencies of its ancestors is calculated, and a topological sort of that graph is printed to STDOUT. This describes the sub-graph of packages that must be built prior to the specified package version. +If the --changes option is used, only recipes that have +been changed and their ancestors will be reported, omitting +duplicates. + 1. https://github.com/conda/conda-build/issues/2467 """ -parser = argparse.ArgumentParser(description=description) +parser = argparse.ArgumentParser( + description=description, + formatter_class=argparse.RawDescriptionHelpFormatter) parser.add_argument("recipes", help="Recipes directory, defaults to current directory", type=str, nargs="?", default=".") parser.add_argument("-p", "--package", type=str, - help="Report dependents (i.e. descendants) of the" + help="Report dependents (i.e. descendants) of the " "specified package") parser.add_argument("-v", "--version", type=str, - help="Report dependents (i.e. descendants) of the" + help="Report dependents (i.e. descendants) of the " "specified package version") +parser.add_argument("-c", "--changes", type=str, default="master", + help="Report only on recipes that have changed " + "relative to another branch (defaults to 'master'") parser.add_argument("--debug", help="Enable DEBUG level logging to STDERR", @@ -338,24 +386,42 @@ def build_dependency_graph(graph, root_node, log.basicConfig(level=level) base = args.recipes +recipe_files = find_recipe_files(base) -pkg_recipes, pkg_versions, pkg_requirements, pkg_outputs = load_recipes(base) +pkg_recipes, pkg_versions, pkg_requirements, pkg_outputs = \ + load_recipes(recipe_files) root_node="root" graph = nx.DiGraph(directed=True) graph = build_dependency_graph(graph, root_node, pkg_versions, pkg_requirements, pkg_outputs) + if args.package and args.version: + # Print a subgraph for a specific package and version pv = (args.package, parse(args.version)) if pv in graph: for node in nx.topological_sort( nx.subgraph(graph, nx.ancestors(graph, pv))): - print(node[0], node[1]) + print_node(node, pkg_recipes) else: raise ValueError("Package {} version {} is not present " "in the graph".format(pv[0], pv[1])) +elif (args.changes): + # Print a unified list of all changed recipes and their ancestors + changed_recipes = find_changed_recipe_files(base, args.changes) + cpkg_recipes, cpkg_versions, cpkg_requirements, cpkg_outputs = \ + load_recipes(changed_recipes) + printed = {} + for cpkg, cversions in cpkg_versions.items(): + for cversion in cversions: + pv = (cpkg, cversion) + if pv in graph: + for node in nx.topological_sort( + nx.subgraph(graph, nx.ancestors(graph, pv))): + if not node in printed: + print_node(node, pkg_recipes) + printed[node] = True else: + # Print everything for node in nx.topological_sort(graph): - if node is not root_node: - recipe = pkg_recipes[node] - print(node[0], node[1], os.path.dirname(recipe)) + print_node(node, pkg_recipes) From 8808139337f612a0944be134ed25471505b36e63 Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 12 Feb 2019 09:15:25 +0000 Subject: [PATCH 047/119] Used $AR and $GCC where appropriate the allow builds to find the Conda build tools. --- recipes/blat/35/build.sh | 17 ++++++++++++++++- recipes/boost/1.68.0/build.sh | 4 ++-- recipes/bwa/0.7.17/build.sh | 3 ++- recipes/freebayes/1.2.0/build.sh | 2 +- recipes/htslib/1.9+47-gc93b673/build.sh | 12 +++++++----- recipes/htslib/1.9+9-g6ec3b94/build.sh | 12 +++++++----- recipes/samtools/1.9+2-g02d93a1/build.sh | 11 ++++++----- recipes/samtools/1.9+37-g5708485/build.sh | 11 ++++++----- recipes/star/2.5.2b/build.sh | 5 +++-- recipes/star/2.5.2b/meta.yaml | 1 + 10 files changed, 51 insertions(+), 27 deletions(-) diff --git a/recipes/blat/35/build.sh b/recipes/blat/35/build.sh index e51eb3e5..9ea66cda 100755 --- a/recipes/blat/35/build.sh +++ b/recipes/blat/35/build.sh @@ -4,11 +4,26 @@ set -ex n="$CPU_COUNT" +# building fails because it has the 'ar' executable name hard-coded +# and doesn't respect Conda's "$AR" environment variable: + +shopt -u | grep -q nullglob && nullglob_enabled=0 +[ $nullglob_enabled ] || shopt -s nullglob + +for f in ar gcc-ar; do + fullname=($BUILD_PREFIX/bin/*-$f) + shortname="$BUILD_PREFIX/bin/$f" + [ -h "$shortname" ] || ln -s "$fullname" "$shortname" +done + +[ $nullglob_enabled ] || shopt -u nullglob + mkdir -p "$SRC_DIR/bin" export XINC="-I$PREFIX/include" make -j $n MACHTYPE=X86_64 BINDIR="$SRC_DIR/bin" \ - CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" + CC="$GCC" \ + CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" mkdir -p "$PREFIX/bin" diff --git a/recipes/boost/1.68.0/build.sh b/recipes/boost/1.68.0/build.sh index 10e17944..c8720c2e 100644 --- a/recipes/boost/1.68.0/build.sh +++ b/recipes/boost/1.68.0/build.sh @@ -4,8 +4,8 @@ set -ex n="$CPU_COUNT" -# bootstrap fails because it has the gcc target name hard-coded as -# 'gcc' and doesn't respect Conda's "$GCC" environment variable: +# bootstrap fails because it has the 'gcc' executable name hard-coded +# and doesn't respect Conda's "$GCC" environment variable: shopt -u | grep -q nullglob && nullglob_enabled=0 [ $nullglob_enabled ] || shopt -s nullglob diff --git a/recipes/bwa/0.7.17/build.sh b/recipes/bwa/0.7.17/build.sh index 5b0ed0e8..d62d3cbe 100755 --- a/recipes/bwa/0.7.17/build.sh +++ b/recipes/bwa/0.7.17/build.sh @@ -4,7 +4,8 @@ set -ex n="$CPU_COUNT" -make -j $n CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make -j $n AR="$AR" CC="$GCC" \ + CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" mkdir -p "$PREFIX/bin" cp bwa "$PREFIX/bin/" diff --git a/recipes/freebayes/1.2.0/build.sh b/recipes/freebayes/1.2.0/build.sh index d27f1446..bcfc2ac7 100755 --- a/recipes/freebayes/1.2.0/build.sh +++ b/recipes/freebayes/1.2.0/build.sh @@ -2,7 +2,7 @@ set -ex -make -j 1 CC="$GCC" CXX="$CXX" LD="$LD" \ +make -j 1 AR="$AR" CC="$GCC" CXX="$CXX" LD="$LD" \ CXXFLAGS="-I$PREFIX/include" \ CPPFLAGS="-I$PREFIX/include" \ LDFLAGS="-L$PREFIX/lib" diff --git a/recipes/htslib/1.9+47-gc93b673/build.sh b/recipes/htslib/1.9+47-gc93b673/build.sh index c404a9d9..612cdad2 100755 --- a/recipes/htslib/1.9+47-gc93b673/build.sh +++ b/recipes/htslib/1.9+47-gc93b673/build.sh @@ -10,11 +10,13 @@ cp aclocal.m4 aclocal.m4.tmp autoreconf cp aclocal.m4.tmp aclocal.m4 -./configure --prefix="$PREFIX" \ - --enable-libcurl \ - --enable-plugins \ - CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make -j $n +CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" \ + ./configure --prefix="$PREFIX" \ + --enable-libcurl \ + --enable-plugins + +make -j $n AR="$AR" CC="$GCC" \ + CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install prefix="$PREFIX" popd diff --git a/recipes/htslib/1.9+9-g6ec3b94/build.sh b/recipes/htslib/1.9+9-g6ec3b94/build.sh index c404a9d9..f3962294 100755 --- a/recipes/htslib/1.9+9-g6ec3b94/build.sh +++ b/recipes/htslib/1.9+9-g6ec3b94/build.sh @@ -10,11 +10,13 @@ cp aclocal.m4 aclocal.m4.tmp autoreconf cp aclocal.m4.tmp aclocal.m4 -./configure --prefix="$PREFIX" \ - --enable-libcurl \ - --enable-plugins \ - CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make -j $n +CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" ./configure \ + --prefix="$PREFIX" \ + --enable-libcurl \ + --enable-plugins + +make -j $n AR="$AR" CC="$GCC" \ + CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install prefix="$PREFIX" popd diff --git a/recipes/samtools/1.9+2-g02d93a1/build.sh b/recipes/samtools/1.9+2-g02d93a1/build.sh index fe272db9..c5daf803 100755 --- a/recipes/samtools/1.9+2-g02d93a1/build.sh +++ b/recipes/samtools/1.9+2-g02d93a1/build.sh @@ -5,12 +5,13 @@ set -ex n="$CPU_COUNT" autoreconf -./configure --prefix="$PREFIX" \ - --with-htslib=system \ - --without-curses \ - CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" \ + ./configure --prefix="$PREFIX" \ + --with-htslib=system \ + --without-curses + +make -j $n AR="$AR" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install prefix="$PREFIX" mkdir p "$PREFIX/include/samtools" diff --git a/recipes/samtools/1.9+37-g5708485/build.sh b/recipes/samtools/1.9+37-g5708485/build.sh index fe272db9..c5daf803 100755 --- a/recipes/samtools/1.9+37-g5708485/build.sh +++ b/recipes/samtools/1.9+37-g5708485/build.sh @@ -5,12 +5,13 @@ set -ex n="$CPU_COUNT" autoreconf -./configure --prefix="$PREFIX" \ - --with-htslib=system \ - --without-curses \ - CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" \ + ./configure --prefix="$PREFIX" \ + --with-htslib=system \ + --without-curses + +make -j $n AR="$AR" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install prefix="$PREFIX" mkdir p "$PREFIX/include/samtools" diff --git a/recipes/star/2.5.2b/build.sh b/recipes/star/2.5.2b/build.sh index c2e2d4a4..5d8af571 100755 --- a/recipes/star/2.5.2b/build.sh +++ b/recipes/star/2.5.2b/build.sh @@ -10,8 +10,9 @@ n="$CPU_COUNT" pushd source make -j $n STAR STARlong \ - CPPFLAGS="-I$SRC_DIR/source/htslib -I$PREFIX/include -DSAMTOOLS=1" \ - LDFLAGSextra="-L$SRC_DIR/source/htslib -L$PREFIX/lib" + CC="$GCC" AR="$AR" \ + CPPFLAGS="-I$SRC_DIR/source/htslib -I$PREFIX/include -DSAMTOOLS=1" \ + LDFLAGSextra="-L$SRC_DIR/source/htslib -L$PREFIX/lib" mkdir -p "$PREFIX/bin" cp STAR "$PREFIX/bin" diff --git a/recipes/star/2.5.2b/meta.yaml b/recipes/star/2.5.2b/meta.yaml index be69cae4..aca1f092 100644 --- a/recipes/star/2.5.2b/meta.yaml +++ b/recipes/star/2.5.2b/meta.yaml @@ -21,6 +21,7 @@ source: requirements: build: - {{ compiler("cxx") }} + - make host: - libz-dev run: From ca805be5b45cc7d71425248b5c2cf72795a84db6 Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 12 Feb 2019 09:19:01 +0000 Subject: [PATCH 048/119] Added Conda build tools where necessary. --- recipes/bowtie/1.0.0_dkj_fopen_with_mm/meta.yaml | 1 + recipes/bowtie/1.2.2/meta.yaml | 1 + recipes/bowtie2/2.2.7/meta.yaml | 1 + recipes/bzip2/1.0.6/meta.yaml | 5 +++++ recipes/crumble/0.8/meta.yaml | 1 + recipes/eigen/3.3.4/meta.yaml | 1 + recipes/fastx_toolkit/0.0.14/meta.yaml | 7 +++++++ recipes/hisat2/2.1.0/meta.yaml | 1 + recipes/io_lib/1.14.11/meta.yaml | 1 + recipes/libgd/2.2.5/meta.yaml | 3 +++ recipes/libxslt/1.1.32/build.sh | 5 ++++- recipes/libxslt/1.1.32/meta.yaml | 3 +++ recipes/minimap2/2.10/meta.yaml | 1 + recipes/xz/5.2.3/meta.yaml | 5 +++++ recipes/zlib/1.2.11/meta.yaml | 3 +-- 15 files changed, 36 insertions(+), 3 deletions(-) diff --git a/recipes/bowtie/1.0.0_dkj_fopen_with_mm/meta.yaml b/recipes/bowtie/1.0.0_dkj_fopen_with_mm/meta.yaml index 18c53f7f..5fc8709e 100644 --- a/recipes/bowtie/1.0.0_dkj_fopen_with_mm/meta.yaml +++ b/recipes/bowtie/1.0.0_dkj_fopen_with_mm/meta.yaml @@ -19,6 +19,7 @@ source: requirements: build: - {{ compiler("cxx") }} + - make test: commands: diff --git a/recipes/bowtie/1.2.2/meta.yaml b/recipes/bowtie/1.2.2/meta.yaml index f7b54ab8..288bf4c9 100644 --- a/recipes/bowtie/1.2.2/meta.yaml +++ b/recipes/bowtie/1.2.2/meta.yaml @@ -19,6 +19,7 @@ source: requirements: build: - gcc # Needs g++ 4.8 + - make host: - tbb-devel - libz-dev diff --git a/recipes/bowtie2/2.2.7/meta.yaml b/recipes/bowtie2/2.2.7/meta.yaml index f5402406..bbf8c98a 100644 --- a/recipes/bowtie2/2.2.7/meta.yaml +++ b/recipes/bowtie2/2.2.7/meta.yaml @@ -19,6 +19,7 @@ source: requirements: build: - {{ compiler("cxx") }} + - make test: commands: diff --git a/recipes/bzip2/1.0.6/meta.yaml b/recipes/bzip2/1.0.6/meta.yaml index e62abaed..63d83ba2 100644 --- a/recipes/bzip2/1.0.6/meta.yaml +++ b/recipes/bzip2/1.0.6/meta.yaml @@ -21,6 +21,11 @@ source: - Makefile.patch - Makefile-libbz2_so.patch +requirements: + build: + - {{ compiler("c") }} + - make + outputs: - name: bzip2 version: {{ version }} diff --git a/recipes/crumble/0.8/meta.yaml b/recipes/crumble/0.8/meta.yaml index 41ea3685..8b9b3392 100644 --- a/recipes/crumble/0.8/meta.yaml +++ b/recipes/crumble/0.8/meta.yaml @@ -20,6 +20,7 @@ source: requirements: build: - {{ compiler("c") }} + - make host: - libhts-dev run: diff --git a/recipes/eigen/3.3.4/meta.yaml b/recipes/eigen/3.3.4/meta.yaml index c54cbf7b..749e0be3 100644 --- a/recipes/eigen/3.3.4/meta.yaml +++ b/recipes/eigen/3.3.4/meta.yaml @@ -21,4 +21,5 @@ requirements: build: - {{ compiler("cxx") }} - cmake + - make diff --git a/recipes/fastx_toolkit/0.0.14/meta.yaml b/recipes/fastx_toolkit/0.0.14/meta.yaml index 2ddba559..3593f341 100644 --- a/recipes/fastx_toolkit/0.0.14/meta.yaml +++ b/recipes/fastx_toolkit/0.0.14/meta.yaml @@ -24,6 +24,12 @@ source: folder: gtextutils sha256: {{ gtextutils_sha256 }} +requirements: + build: + - {{ compiler("cxx") }} + - make + - pkg-config + outputs: - name: fastx_toolkit version: {{ version }} @@ -31,6 +37,7 @@ outputs: build: - {{ compiler("cxx") }} - make + - pkg-config files: - bin/fast* diff --git a/recipes/hisat2/2.1.0/meta.yaml b/recipes/hisat2/2.1.0/meta.yaml index 6a7ad08a..4afc76d9 100644 --- a/recipes/hisat2/2.1.0/meta.yaml +++ b/recipes/hisat2/2.1.0/meta.yaml @@ -23,6 +23,7 @@ source: requirements: build: - {{ compiler("cxx") }} + - make host: - libz-dev run: diff --git a/recipes/io_lib/1.14.11/meta.yaml b/recipes/io_lib/1.14.11/meta.yaml index 2ace732c..b63e9bf6 100644 --- a/recipes/io_lib/1.14.11/meta.yaml +++ b/recipes/io_lib/1.14.11/meta.yaml @@ -22,6 +22,7 @@ requirements: build: - {{ compiler("c") }} - autoconf + - make host: - irods-dev >=4.1.12 - libbz2-dev diff --git a/recipes/libgd/2.2.5/meta.yaml b/recipes/libgd/2.2.5/meta.yaml index cf375ffc..2474768f 100644 --- a/recipes/libgd/2.2.5/meta.yaml +++ b/recipes/libgd/2.2.5/meta.yaml @@ -22,6 +22,7 @@ requirements: build: - {{ compiler("c") }} - libtool + - make - pkg-config host: - libpng-dev @@ -37,6 +38,7 @@ outputs: build: - {{ compiler("c") }} - libtool + - make - pkg-config host: - libpng-dev @@ -58,6 +60,7 @@ outputs: build: - {{ compiler("c") }} - libtool + - make - pkg-config host: - libpng-dev diff --git a/recipes/libxslt/1.1.32/build.sh b/recipes/libxslt/1.1.32/build.sh index 6bd4ca82..989992c2 100644 --- a/recipes/libxslt/1.1.32/build.sh +++ b/recipes/libxslt/1.1.32/build.sh @@ -4,7 +4,10 @@ set -ex n="$CPU_COUNT" -./configure prefix="$PREFIX" --without-python +./configure prefix="$PREFIX" \ + --without-crypto \ + --without-python make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install + diff --git a/recipes/libxslt/1.1.32/meta.yaml b/recipes/libxslt/1.1.32/meta.yaml index 7917a1bc..eda40b99 100644 --- a/recipes/libxslt/1.1.32/meta.yaml +++ b/recipes/libxslt/1.1.32/meta.yaml @@ -22,6 +22,7 @@ requirements: build: - {{ compiler("c") }} - make + - pkg-config host: - liblzma-dev - libxml2-dev @@ -38,6 +39,7 @@ outputs: build: - {{ compiler("c") }} - make + - pkg-config host: - liblzma-dev - libxml2-dev @@ -59,6 +61,7 @@ outputs: build: - {{ compiler("c") }} - make + - pkg-config host: - liblzma-dev - libxml2-dev diff --git a/recipes/minimap2/2.10/meta.yaml b/recipes/minimap2/2.10/meta.yaml index cfd40f30..4accb55c 100644 --- a/recipes/minimap2/2.10/meta.yaml +++ b/recipes/minimap2/2.10/meta.yaml @@ -22,6 +22,7 @@ source: requirements: build: - {{ compiler("c") }} + - make host: - libz-dev run: diff --git a/recipes/xz/5.2.3/meta.yaml b/recipes/xz/5.2.3/meta.yaml index f6563524..cf76c865 100644 --- a/recipes/xz/5.2.3/meta.yaml +++ b/recipes/xz/5.2.3/meta.yaml @@ -18,6 +18,11 @@ source: fn: xz-{{ version }}.tar.bz2 sha256: {{ sha256 }} +requirements: + build: + - {{ compiler("c") }} + - make + outputs: - name: xz version: {{ version }} diff --git a/recipes/zlib/1.2.11/meta.yaml b/recipes/zlib/1.2.11/meta.yaml index e7e3058b..ff4ccecf 100644 --- a/recipes/zlib/1.2.11/meta.yaml +++ b/recipes/zlib/1.2.11/meta.yaml @@ -21,8 +21,7 @@ source: requirements: build: - {{ compiler("c") }} - run: - - {{ pin_subpackage('libz-dev', exact=True) }} + - make outputs: - name: libz From 80a9a9a5843febee5d565eeff1468e54de4b349f Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 12 Feb 2019 09:21:58 +0000 Subject: [PATCH 049/119] Removed s3cmd and python-magic dependency. --- recipes/python-magic/0.4.15/README.md | 3 -- recipes/python-magic/0.4.15/build.sh | 5 --- recipes/python-magic/0.4.15/meta.yaml | 30 ----------------- recipes/s3cmd/2.0.1-28-gd5e61c3/README.md | 3 -- recipes/s3cmd/2.0.1-28-gd5e61c3/build.sh | 5 --- recipes/s3cmd/2.0.1-28-gd5e61c3/meta.yaml | 36 --------------------- recipes/s3cmd/2.0.1-28-gd5e61c3/s3cmd.patch | 16 --------- 7 files changed, 98 deletions(-) delete mode 100644 recipes/python-magic/0.4.15/README.md delete mode 100644 recipes/python-magic/0.4.15/build.sh delete mode 100644 recipes/python-magic/0.4.15/meta.yaml delete mode 100644 recipes/s3cmd/2.0.1-28-gd5e61c3/README.md delete mode 100644 recipes/s3cmd/2.0.1-28-gd5e61c3/build.sh delete mode 100644 recipes/s3cmd/2.0.1-28-gd5e61c3/meta.yaml delete mode 100644 recipes/s3cmd/2.0.1-28-gd5e61c3/s3cmd.patch diff --git a/recipes/python-magic/0.4.15/README.md b/recipes/python-magic/0.4.15/README.md deleted file mode 100644 index ec89dc5f..00000000 --- a/recipes/python-magic/0.4.15/README.md +++ /dev/null @@ -1,3 +0,0 @@ - -N.B. This build relies on libmagic being installed by the OS package -manager (or other means). diff --git a/recipes/python-magic/0.4.15/build.sh b/recipes/python-magic/0.4.15/build.sh deleted file mode 100644 index e011b675..00000000 --- a/recipes/python-magic/0.4.15/build.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/sh - -set -e - -$PYTHON setup.py install diff --git a/recipes/python-magic/0.4.15/meta.yaml b/recipes/python-magic/0.4.15/meta.yaml deleted file mode 100644 index 49486f3d..00000000 --- a/recipes/python-magic/0.4.15/meta.yaml +++ /dev/null @@ -1,30 +0,0 @@ -{% set version = "0.4.15" %} -{% set sha256 = "6d730389249ab1e34ffb0a3c5beaa44e116687ffa081e0176dab6c59ff271593" %} - -package: - name: python-magic - version: "{{ version }}" - -about: - home: https://github.com/ahupp/python-magic - license: MIT - summary: "A python wrapper for libmagic." - -build: - number: 1 - -source: - url: https://github.com/ahupp/python-magic/archive/{{ version }}.tar.gz - fn: python-magic-{{ version }}.tar.gz - sha256: {{ sha256 }} - -requirements: - host: - - python - - setuptools - run: - - python - -test: - imports: - - magic diff --git a/recipes/s3cmd/2.0.1-28-gd5e61c3/README.md b/recipes/s3cmd/2.0.1-28-gd5e61c3/README.md deleted file mode 100644 index cf550630..00000000 --- a/recipes/s3cmd/2.0.1-28-gd5e61c3/README.md +++ /dev/null @@ -1,3 +0,0 @@ - -This version is built from the HEAD of master, with Matthew Vernon's -patch applied. See https://github.com/s3tools/s3cmd/pull/973 diff --git a/recipes/s3cmd/2.0.1-28-gd5e61c3/build.sh b/recipes/s3cmd/2.0.1-28-gd5e61c3/build.sh deleted file mode 100644 index a58b8225..00000000 --- a/recipes/s3cmd/2.0.1-28-gd5e61c3/build.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/sh - -set -ex - -$PYTHON setup.py install diff --git a/recipes/s3cmd/2.0.1-28-gd5e61c3/meta.yaml b/recipes/s3cmd/2.0.1-28-gd5e61c3/meta.yaml deleted file mode 100644 index ff9fd276..00000000 --- a/recipes/s3cmd/2.0.1-28-gd5e61c3/meta.yaml +++ /dev/null @@ -1,36 +0,0 @@ -{% set version = "2.0.1_28_gd5e61c3" %} - -package: - name: s3cmd - version: "{{ version }}" - -about: - home: https://github.com/s3tools/s3cmd - license: GPLv2 - summary: "Command line tool for managing Amazon S3 and CloudFront services." - -build: - number: 0 - -source: - git_url: https://github.com/s3tools/s3cmd.git - git_rev: d5e61c3eb02a9b4e66d49fa0f1ad8279d007994b - - patches: - - s3cmd.patch - -requirements: - build: - - python - - python-dateutil - - python-magic - - setuptools - - run: - - python - - python-dateutil - - python-magic - -test: - commands: - - s3cmd --help diff --git a/recipes/s3cmd/2.0.1-28-gd5e61c3/s3cmd.patch b/recipes/s3cmd/2.0.1-28-gd5e61c3/s3cmd.patch deleted file mode 100644 index 74648b6a..00000000 --- a/recipes/s3cmd/2.0.1-28-gd5e61c3/s3cmd.patch +++ /dev/null @@ -1,16 +0,0 @@ -diff --git a/S3/ACL.py b/S3/ACL.py -index 175725a8..7f4d2455 100644 ---- a/S3/ACL.py -+++ b/S3/ACL.py -@@ -186,9 +186,9 @@ def revoke(self, name, permission): - permission = permission.upper() - - if "ALL" == permission: -- self.grantees = [g for g in self.grantees if not (g.name.lower() == name or g.display_name.lower() == name)] -+ self.grantees = [g for g in self.grantees if not (g.name.lower() == name or (g.display_name is not None and g.display_name.lower() == name))] - else: -- self.grantees = [g for g in self.grantees if not ((g.display_name.lower() == name or g.name.lower() == name) -+ self.grantees = [g for g in self.grantees if not (((g.display_name is not None and g.display_name.lower() == name) or g.name.lower() == name) - and g.permission.upper() == permission)] - - def get_printable_tree(self): From 4f4e4b9cfa6aae97083a8f98afbead59009977e5 Mon Sep 17 00:00:00 2001 From: Keith James Date: Wed, 13 Feb 2019 09:14:59 +0000 Subject: [PATCH 050/119] Bambi release 0.11.2 (fixes integer overflow in Bambi, https://github.com/wtsi-npg/bambi/pull/133) --- recipes/bambi/0.11.2/build.sh | 12 ++++++++++++ recipes/bambi/0.11.2/meta.yaml | 35 ++++++++++++++++++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100755 recipes/bambi/0.11.2/build.sh create mode 100644 recipes/bambi/0.11.2/meta.yaml diff --git a/recipes/bambi/0.11.2/build.sh b/recipes/bambi/0.11.2/build.sh new file mode 100755 index 00000000..1a1c597a --- /dev/null +++ b/recipes/bambi/0.11.2/build.sh @@ -0,0 +1,12 @@ +#!/bin/sh + +set -e + +autoreconf -fi + +n=`expr $CPU_COUNT / 4 \| 1` + +./configure --prefix="$PREFIX" --with-htslib="$PREFIX" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" + +make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make install prefix="$PREFIX" diff --git a/recipes/bambi/0.11.2/meta.yaml b/recipes/bambi/0.11.2/meta.yaml new file mode 100644 index 00000000..5172fa3a --- /dev/null +++ b/recipes/bambi/0.11.2/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.11.2" %} +{% set htslib_version = "1.9+66_gbcf9bff" %} + + +package: + name: bambi + version: "{{ version }}" + +about: + home: https://github.com/wtsi-npg/bambi + license: AGPL + summary: "A set of programs to manipulate SAM/BAM/CRAM files, using HTSLIB." + +build: + number: 0 + +source: + git_url: https://github.com/wtsi-npg/bambi.git + git_rev: 0.11.2 + +requirements: + build: + - gcc_npg >=7.3 + - htslib =={{ htslib_version }} + - libgd + - libxml2 + + run: + - htslib =={{ htslib_version }} + - libgd + - libxml2 + +test: + commands: + - bambi --version From 219b747b6a9d2a1f7f6be5b0d0761848042e227e Mon Sep 17 00:00:00 2001 From: Keith James Date: Thu, 14 Feb 2019 16:55:12 +0000 Subject: [PATCH 051/119] Fixed two requirements lists that were missing their YAML list token. --- recipes/baton/1.1.0/meta.yaml | 2 +- recipes/libxml2/2.9.7/meta.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/baton/1.1.0/meta.yaml b/recipes/baton/1.1.0/meta.yaml index 6f052d77..985d8562 100644 --- a/recipes/baton/1.1.0/meta.yaml +++ b/recipes/baton/1.1.0/meta.yaml @@ -93,7 +93,7 @@ outputs: version: {{ version }} requirements: run: - {{ pin_subpackage("libbaton", exact=True) }} + - {{ pin_subpackage("libbaton", exact=True) }} files: - include/baton - lib/pkgconfig/baton.pc diff --git a/recipes/libxml2/2.9.7/meta.yaml b/recipes/libxml2/2.9.7/meta.yaml index 65cae452..3d158e36 100644 --- a/recipes/libxml2/2.9.7/meta.yaml +++ b/recipes/libxml2/2.9.7/meta.yaml @@ -72,7 +72,7 @@ outputs: - name: libxml2-dev requirements: run: - {{ pin_subpackage('libxml2', exact=True) }} + - {{ pin_subpackage('libxml2', exact=True) }} files: - include/libxml2 - lib/xml2Conf.sh From d57655704e141bb3acf6f38ea168f930772347c0 Mon Sep 17 00:00:00 2001 From: Keith James Date: Thu, 14 Feb 2019 17:03:13 +0000 Subject: [PATCH 052/119] Fixed bug caused by having a default value for the --changes CLI option (now an argument must be provided). Improved filtering of Jinjer2 macro "None" values from input. --- scripts/package_sort.py | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/scripts/package_sort.py b/scripts/package_sort.py index dd0eddd6..2156dcab 100755 --- a/scripts/package_sort.py +++ b/scripts/package_sort.py @@ -244,18 +244,23 @@ def add_listval(dikt, key, value): for output in outputs: output_name = output["name"] pkg_outputs[output_name] = pkg_name - output_reqs = output.get("requirements", {}) + pkg_reqs += output_reqs.get("host", []) pkg_reqs += output_reqs.get("run", []) + pkg_reqs = list(set(pkg_reqs)) + # Jinja2 macros appear as 'None' - filter any of these out + pkg_reqs = [x for x in pkg_reqs if x != "None"] + + log.debug("Requirements for %s are: %s", pkg_name, pkg_reqs) + for pkg_req in pkg_reqs: req, spec = parse_requirement(pkg_req) - if req is not 'None': - log.debug("%s version: %s requires %s version: %s", - pkg_name, pkg_version, req, spec) - add_listval(pkg_requirements, (pkg_name, pkg_version), - (req, spec)) + log.debug("%s version: %s requires %s version: %s", + pkg_name, pkg_version, req, spec) + add_listval(pkg_requirements, (pkg_name, pkg_version), + (req, spec)) return pkg_recipes, pkg_versions, pkg_requirements, pkg_outputs @@ -365,7 +370,7 @@ def print_node(node, pkg_recipes): parser.add_argument("-v", "--version", type=str, help="Report dependents (i.e. descendants) of the " "specified package version") -parser.add_argument("-c", "--changes", type=str, default="master", +parser.add_argument("-c", "--changes", type=str, help="Report only on recipes that have changed " "relative to another branch (defaults to 'master'") From b6cdadc18c245cb58017013953c2917f2352eca4 Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 19 Feb 2019 14:32:10 +0000 Subject: [PATCH 053/119] Refactored compiler environment variables. I was forced to use LD_LIBRARY_PATH during configure to allow autoconf's conftest programs to find Conda-hosted libraries in the build environment. I'm pretty sure I shouldn't have to do this (tried -rpath and -rpath-link too). --- recipes/baton/1.1.0/build.sh | 11 +++++++---- recipes/tears/1.2.4/build.sh | 8 +++++--- 2 files changed, 12 insertions(+), 7 deletions(-) diff --git a/recipes/baton/1.1.0/build.sh b/recipes/baton/1.1.0/build.sh index db65188a..b2dd5785 100755 --- a/recipes/baton/1.1.0/build.sh +++ b/recipes/baton/1.1.0/build.sh @@ -4,10 +4,13 @@ set -ex n="$CPU_COUNT" -./configure --prefix="$PREFIX" --with-irods="$PREFIX" \ - CPPFLAGS="-I$PREFIX/include -I$PREFIX/include/irods" \ - LDFLAGS="-L$PREFIX/lib -L$PREFIX/lib/irods/externals" +export LD_LIBRARY_PATH="$PREFIX/lib" -make -j $n CPPFLAGS="-I$PREFIX/include -I$PREFIX/include/irods" \ +CPPFLAGS="-I$PREFIX/include -I$PREFIX/include/irods" \ + LDFLAGS="-L$PREFIX/lib -L$PREFIX/lib/irods/externals" \ + ./configure --prefix="$PREFIX" --with-irods="$PREFIX" + +make -j $n \ + CPPFLAGS="-I$PREFIX/include -I$PREFIX/include/irods" \ LDFLAGS="-L$PREFIX/lib -L$PREFIX/lib/irods/externals" make install prefix="$PREFIX" diff --git a/recipes/tears/1.2.4/build.sh b/recipes/tears/1.2.4/build.sh index 0ebf96da..f1806a9f 100755 --- a/recipes/tears/1.2.4/build.sh +++ b/recipes/tears/1.2.4/build.sh @@ -4,9 +4,11 @@ set -ex autoreconf -fi -./configure --prefix="$PREFIX" --with-irods="$PREFIX" \ - CPPFLAGS="-I$PREFIX/include -I$PREFIX/include/irods" \ - LDFLAGS="-L$PREFIX/lib -L$PREFIX/lib/irods/externals" +export LD_LIBRARY_PATH="$PREFIX/lib" + +CPPFLAGS="-I$PREFIX/include -I$PREFIX/include/irods" \ + LDFLAGS="-L$PREFIX/lib -L$PREFIX/lib/irods/externals" \ + ./configure --prefix="$PREFIX" --with-irods="$PREFIX" make CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install prefix="$PREFIX" From 51570dd2c45b0ca3f1cfeaecdf14984a25bfa4f0 Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 19 Feb 2019 15:20:26 +0000 Subject: [PATCH 054/119] Avoid trying to install iRODS dependency packages when running in Docker where the user is conda, not root. --- recipes/irods/4.1.12/build.sh | 26 +++++++++++++++++++++----- 1 file changed, 21 insertions(+), 5 deletions(-) diff --git a/recipes/irods/4.1.12/build.sh b/recipes/irods/4.1.12/build.sh index 0f06b0c9..2b21ee77 100644 --- a/recipes/irods/4.1.12/build.sh +++ b/recipes/irods/4.1.12/build.sh @@ -23,6 +23,14 @@ unrpm_data() { rm -r ./tmp } +running_in_docker() { + if [ -f /.dockerenv ]; then + return 0 + else + return 1 + fi +} + install_gcc_ubuntu() { GCC_VERSION= grep precise /etc/lsb-release && GCC_VERSION="4.6" @@ -74,9 +82,13 @@ export TERM=dumb git submodule init && git submodule update if [ -f /etc/lsb-release ]; then - install_gcc_ubuntu - install_deps_ubuntu - + if running_in_docker ; then + echo "Running in Docker ... skipping package installation" + else + install_gcc_ubuntu + install_deps_ubuntu + fi + ./packaging/build.sh --verbose icat postgres ./packaging/build.sh --verbose icommands @@ -90,8 +102,12 @@ if [ -f /etc/lsb-release ]; then fi if [ -f /etc/redhat-release ]; then - install_gcc_rhel - install_deps_rhel + if running_in_docker ; then + echo "Running in Docker ... skipping package installation" + else + install_gcc_rhel + install_deps_rhel + fi ./packaging/build.sh --verbose icat postgres ./packaging/build.sh --verbose icommands From a0a62e903b7c9a4f3c124e97a9f3215421511ebe Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 19 Feb 2019 15:21:56 +0000 Subject: [PATCH 055/119] Use the Conda compilers, but configure to a suitably old C++ standard. --- recipes/bowtie/1.2.2/conda_build_config.yaml | 6 ++---- recipes/bowtie/1.2.2/meta.yaml | 2 +- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/recipes/bowtie/1.2.2/conda_build_config.yaml b/recipes/bowtie/1.2.2/conda_build_config.yaml index 54d7f516..bd154b47 100644 --- a/recipes/bowtie/1.2.2/conda_build_config.yaml +++ b/recipes/bowtie/1.2.2/conda_build_config.yaml @@ -1,5 +1,3 @@ -c_compiler_version: - - 5.4 -cxx_compiler_version: - - 5.4 +# Set -std=c++03 (see https://github.com/BenLangmead/bowtie/issues/76) +CXXFLAGS: "-march=x86-64 -mtune=generic -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -std=c++03" diff --git a/recipes/bowtie/1.2.2/meta.yaml b/recipes/bowtie/1.2.2/meta.yaml index 288bf4c9..37b46d9a 100644 --- a/recipes/bowtie/1.2.2/meta.yaml +++ b/recipes/bowtie/1.2.2/meta.yaml @@ -18,7 +18,7 @@ source: requirements: build: - - gcc # Needs g++ 4.8 + - {{ compiler("cxx") }} - make host: - tbb-devel From fbfc1b61213a24be7e30fe9d6830f72dcd1e9968 Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Wed, 20 Feb 2019 14:16:34 +0000 Subject: [PATCH 056/119] Added wr 0.17.0 --- recipes/wr/0.17.0/build.sh | 12 ++++++++++++ recipes/wr/0.17.0/meta.yaml | 24 ++++++++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 recipes/wr/0.17.0/build.sh create mode 100644 recipes/wr/0.17.0/meta.yaml diff --git a/recipes/wr/0.17.0/build.sh b/recipes/wr/0.17.0/build.sh new file mode 100644 index 00000000..f093a2c3 --- /dev/null +++ b/recipes/wr/0.17.0/build.sh @@ -0,0 +1,12 @@ +#!/bin/sh + +set -e + +mkdir -p "$PREFIX/bin" +cp wr "$PREFIX/bin/" + +mkdir -p "$PREFIX/etc" +cp wr_config.yml "$PREFIX/etc/" + +mkdir -p "$PREFIX/share/doc/wr" +cp README.md "$PREFIX/share/doc/wr/" diff --git a/recipes/wr/0.17.0/meta.yaml b/recipes/wr/0.17.0/meta.yaml new file mode 100644 index 00000000..8ed46a5a --- /dev/null +++ b/recipes/wr/0.17.0/meta.yaml @@ -0,0 +1,24 @@ +{% set version = "0.17.0" %} +{% set sha256 = "70fe3adde9756195450fb436280bac22266109ee43d4e58fc58d15cf8f309ab0" %} + +package: + name: wr + version: "{{ version }}" + +about: + home: https://github.com/VertebrateResequencing/wr + license: GPLv3 + summary: "High performance Workflow Runner." + +build: + number: 0 + binary_relocation: false + +source: + url: https://github.com/VertebrateResequencing/wr/releases/download/v{{ version }}/wr-linux-x86-64.zip + fn: wr-{{ version }}.zip + sha256: {{ sha256 }} + +test: + commands: + - wr -h From 6b20829afbcd1229e19d2a63903dd0d797b484ef Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 25 Feb 2019 16:57:36 +0000 Subject: [PATCH 057/119] Added a basic build script. --- scripts/build.py | 46 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100755 scripts/build.py diff --git a/scripts/build.py b/scripts/build.py new file mode 100755 index 00000000..e2a4ac14 --- /dev/null +++ b/scripts/build.py @@ -0,0 +1,46 @@ +#!/usr/bin/env python3 + +# Usage: ./scripts/package_sort.py [args] | ./scripts/build.py + +import os +import sys +import subprocess +import time + +def docker_pull(image): + subprocess.check_output(['docker', 'pull', image]) + +RECIPES_DIR=os.path.expandvars("$HOME/conda-recipes") +ARTEFACTS_DIR=os.path.expandvars("$HOME/conda-artefacts") +CONDA_RECIPES_MOUNT="/home/conda/recipes" +CONDA_BUILD_MOUNT="/opt/conda/conda-bld" + +IRODS_BUILD_IMAGE="wsinpg/conda-irods-12.04:0.2" +docker_pull(IRODS_BUILD_IMAGE) + +CONDA_BUILD_IMAGE="wsinpg/conda-12.04:0.2" +docker_pull(CONDA_BUILD_IMAGE) + +for line in sys.stdin.readlines(): + line.rstrip(); + name, version, path = line.split() + print("%s %s %s" % (name, version, path)) + + build_image = CONDA_BUILD_IMAGE + if name == "irods": + build_image = IRODS_BUILD_IMAGE + print("Using image %s" % build_image) + + build_script = 'export CONDA_BLD_PATH="%s" ; ' \ + 'cd "%s/npg_conda" && conda build %s' % \ + (CONDA_BUILD_MOUNT, CONDA_RECIPES_MOUNT, path) + + subprocess.check_output( + ['docker', 'run', + '--mount', + 'source=%s,target=%s,type=bind' % (RECIPES_DIR, CONDA_RECIPES_MOUNT), + '--mount', + 'source=%s,target=%s,type=bind' % (ARTEFACTS_DIR, CONDA_BUILD_MOUNT), + '-i', '-e', 'CONDA_USER_ID=1000', + build_image, + 'sh', '-c', build_script]) From 6e503f9e06e2d8addf7942980b9686788276a367 Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 26 Feb 2019 17:19:28 +0000 Subject: [PATCH 058/119] Correct the --changes option of package_sort.py to print only the changed recipe(s) rather than their ancestors. Use python rather than python3 in shebang lines. Added Travis CI config. Added logging of changed recipes. Added CLI options to build.py for configuration. Decode and split raw command output for clarity in build.py if there are errors (it can be large). Exit with failure on errors, but build as many recipes as possible. Updated zlib license. --- .travis.yml | 37 ++++++++ recipes/zlib/1.2.11/meta.yaml | 2 +- scripts/build.py | 162 ++++++++++++++++++++++++++++------ scripts/package_sort.py | 25 +++--- 4 files changed, 186 insertions(+), 40 deletions(-) create mode 100644 .travis.yml diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 00000000..ff51711e --- /dev/null +++ b/.travis.yml @@ -0,0 +1,37 @@ + +dist: xenial +language: python +python: 3.7 + +services: docker + +env: + - > + IRODS_IMAGE=wsinpg/conda-irods-12.04:0.2 + CONDA_IMAGE=wsinpg/conda-12.04:0.2 + COMPARE_BRANCH=origin/devel + +before_install: + - docker --version + # We should rarely need to pull the iRODS build image, so we don't + # do it preemptively here + - docker pull $CONDA_IMAGE + +install: + - pip install jinja2 networkx packaging pyaml setuptools + # Ensure we have a complete repository to compare diffs with other + # branches + - git config remote.origin.fetch +refs/heads/*:refs/remotes/origin/* + - git fetch + +script: + - mkdir -p $TRAVIS_BUILD_DIR/conda-artefacts + - while sleep 300; do echo $SECONDS sec elapsed, still building ... ; done & + - > + ./scripts/package_sort.py --changes $COMPARE_BRANCH | ./scripts/build.py + --recipes-dir $TRAVIS_BUILD_DIR + --artefacts-dir $TRAVIS_BUILD_DIR/conda-artefacts + --irods-build-image $IRODS_IMAGE + --conda-build-image $CONDA_IMAGE --verbose + - kill %1 + - ls -l $TRAVIS_BUILD_DIR/conda-artefacts/linux-64 diff --git a/recipes/zlib/1.2.11/meta.yaml b/recipes/zlib/1.2.11/meta.yaml index ff4ccecf..cd1fd0c9 100644 --- a/recipes/zlib/1.2.11/meta.yaml +++ b/recipes/zlib/1.2.11/meta.yaml @@ -7,7 +7,7 @@ package: about: home: http://zlib.net/ - license: zlib + license: Other summary: A Massively Spiffy Yet Delicately Unobtrusive Compression Library. build: diff --git a/scripts/build.py b/scripts/build.py index e2a4ac14..2ed9279a 100755 --- a/scripts/build.py +++ b/scripts/build.py @@ -1,46 +1,154 @@ -#!/usr/bin/env python3 +#!/usr/bin/env python +# +# Copyright © 2019 Genome Research Ltd. All rights reserved. +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +# +# @author Keith James -# Usage: ./scripts/package_sort.py [args] | ./scripts/build.py +import logging as log +import argparse import os import sys import subprocess import time + def docker_pull(image): subprocess.check_output(['docker', 'pull', image]) -RECIPES_DIR=os.path.expandvars("$HOME/conda-recipes") -ARTEFACTS_DIR=os.path.expandvars("$HOME/conda-artefacts") -CONDA_RECIPES_MOUNT="/home/conda/recipes" -CONDA_BUILD_MOUNT="/opt/conda/conda-bld" + +DEFAULT_RECIPES_DIR=os.path.expandvars("$HOME/conda-recipes") +DEFAULT_RECIPES_MOUNT="/home/conda/recipes" + +DEFAULT_ARTEFACTS_DIR=os.path.expandvars("$HOME/conda-artefacts") +DEFAULT_ARTEFACTS_MOUNT="/opt/conda/conda-bld" IRODS_BUILD_IMAGE="wsinpg/conda-irods-12.04:0.2" -docker_pull(IRODS_BUILD_IMAGE) +DEFAULT_BUILD_IMAGE="wsinpg/conda-12.04:0.2" + +CONDA_CHANNEL="https://dnap.cog.sanger.ac.uk/npg/conda/devel/" + +description = """ + +Runs conda build in the specified Docker image. This script expects +input on STDIN consisting of 3 whitespace-separated fields per line +for each package to be built: + + + +This input is normally generated by the accompanying package_sort.py +script which sorts packages so that dependencies are built first. + +""" + +parser = argparse.ArgumentParser( + description=description, + formatter_class=argparse.RawDescriptionHelpFormatter) -CONDA_BUILD_IMAGE="wsinpg/conda-12.04:0.2" -docker_pull(CONDA_BUILD_IMAGE) +parser.add_argument("--recipes-dir", + help="Host recipes directory, " + "defaults to {}".format(DEFAULT_RECIPES_DIR), + type=str, nargs="?", default=DEFAULT_RECIPES_DIR) +parser.add_argument("--recipes-mount", + help="Container recipes mount, " + "defaults to {}".format(DEFAULT_RECIPES_MOUNT), + type=str, nargs="?", default=DEFAULT_RECIPES_MOUNT) + +parser.add_argument("--artefacts-dir", + help="Host build artefacts directory, " + "defaults to {}".format(DEFAULT_ARTEFACTS_DIR), + type=str, nargs="?", default=DEFAULT_ARTEFACTS_DIR) +parser.add_argument("--artefacts-mount", + help="Container build artefacts mount, " + "defaults to {}".format(DEFAULT_ARTEFACTS_MOUNT), + type=str, nargs="?", default=DEFAULT_ARTEFACTS_MOUNT) + +parser.add_argument("--irods-build-image", + help="The Docker image used to build iRODS, " + "defaults to {}".format(IRODS_BUILD_IMAGE), + type=str, nargs="?", default=IRODS_BUILD_IMAGE) +parser.add_argument("--conda-build-image", + help="Docker image used to build packages, " + "defaults to {}".format(DEFAULT_BUILD_IMAGE), + type=str, nargs="?", default=DEFAULT_BUILD_IMAGE) + +parser.add_argument("--dry-run", + help="Log the recipes that would be built at INFO level, " + "but do not build anything", + action="store_true") +parser.add_argument("--debug", + help="Enable DEBUG level logging to STDERR", + action="store_true") +parser.add_argument("--verbose", + help="Enable INFO level logging to STDERR", + action="store_true") + +args = parser.parse_args() + +level = log.ERROR +if args.debug: + level = log.DEBUG +elif args.verbose or args.dry_run: + level = log.INFO +log.basicConfig(level=level) + +docker_pull(args.conda_build_image) + +fail = False for line in sys.stdin.readlines(): line.rstrip(); name, version, path = line.split() - print("%s %s %s" % (name, version, path)) + log.info("Working on %s %s %s", name, version, path) - build_image = CONDA_BUILD_IMAGE + build_image = args.conda_build_image if name == "irods": - build_image = IRODS_BUILD_IMAGE - print("Using image %s" % build_image) - - build_script = 'export CONDA_BLD_PATH="%s" ; ' \ - 'cd "%s/npg_conda" && conda build %s' % \ - (CONDA_BUILD_MOUNT, CONDA_RECIPES_MOUNT, path) - - subprocess.check_output( - ['docker', 'run', - '--mount', - 'source=%s,target=%s,type=bind' % (RECIPES_DIR, CONDA_RECIPES_MOUNT), - '--mount', - 'source=%s,target=%s,type=bind' % (ARTEFACTS_DIR, CONDA_BUILD_MOUNT), - '-i', '-e', 'CONDA_USER_ID=1000', - build_image, - 'sh', '-c', build_script]) + build_image = args.irods_build_image + log.info("Using image %s", build_image) + docker_pull(args.irods_build_image) + + build_script = \ + 'export CONDA_BLD_PATH="{}" ; ' \ + 'conda config --set auto_update_conda False ; ' \ + 'conda config --add channels {} ; ' \ + 'cd "{}" && conda build {}'.format(args.artefacts_mount, + CONDA_CHANNEL, + args.recipes_mount, + path) + if args.dry_run: + log.info('Build script: "%s"', build_script) + else: + log.debug('Build script: "%s"', build_script) + + try: + subprocess.check_output( + ['docker', 'run', + '--mount', + 'source={},target={},type=bind'.format(args.recipes_dir, + args.recipes_mount), + '--mount', + 'source={},target={},type=bind'.format(args.artefacts_dir, + args.artefacts_mount), + '-i', '-e', 'CONDA_USER_ID=1000', + build_image, + '/bin/sh', '-c', build_script], stderr=subprocess.STDOUT) + except subprocess.CalledProcessError as e: + fail = True + for line in e.output.decode("utf-8").split("\n"): + log.error(line) + +if fail: + exit(1) diff --git a/scripts/package_sort.py b/scripts/package_sort.py index 2156dcab..93b5b225 100755 --- a/scripts/package_sort.py +++ b/scripts/package_sort.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python3 +#!/usr/bin/env python # # Copyright © 2018, 2019 Genome Research Ltd. All rights reserved. # @@ -95,10 +95,14 @@ def find_changed_recipe_files(dir, branch="master"): :rtype: list str """ - proc = subprocess.Popen(["git", "diff", "--name-only", - "--diff-filter=d", branch, dir], - stdout=subprocess.PIPE) - files = [line.rstrip().decode("utf-8") for line in proc.stdout] + try: + out = subprocess.check_output(["git", "diff", "--name-only", + "--diff-filter=d", branch, dir]) + except subprocess.CalledProcessError as e: + log.error(e.output) + raise e + + files = [line.rstrip() for line in out.decode("utf-8").split("\n")] dirs = list(set([os.path.dirname(f) for f in files])) dirs.sort() @@ -107,6 +111,8 @@ def find_changed_recipe_files(dir, branch="master"): recipe = os.path.join(dir, "meta.yaml") if (os.path.isfile(recipe)): recipe_files.append(recipe) + + log.info("Recipes changed relative to %s: %s", branch, recipe_files) return recipe_files @@ -412,20 +418,15 @@ def print_node(node, pkg_recipes): raise ValueError("Package {} version {} is not present " "in the graph".format(pv[0], pv[1])) elif (args.changes): - # Print a unified list of all changed recipes and their ancestors + # Print a unified list of all changed recipes changed_recipes = find_changed_recipe_files(base, args.changes) cpkg_recipes, cpkg_versions, cpkg_requirements, cpkg_outputs = \ load_recipes(changed_recipes) - printed = {} for cpkg, cversions in cpkg_versions.items(): for cversion in cversions: pv = (cpkg, cversion) if pv in graph: - for node in nx.topological_sort( - nx.subgraph(graph, nx.ancestors(graph, pv))): - if not node in printed: - print_node(node, pkg_recipes) - printed[node] = True + print_node(pv, pkg_recipes) else: # Print everything for node in nx.topological_sort(graph): From 3caf3da5ec95823da2b7f1902f8405b099d96183 Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 26 Feb 2019 17:28:18 +0000 Subject: [PATCH 059/119] Added missing build tool dependency on Conda make. --- recipes/bam_stats/1.13.0/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/bam_stats/1.13.0/meta.yaml b/recipes/bam_stats/1.13.0/meta.yaml index ebddd8c5..ac5281a4 100644 --- a/recipes/bam_stats/1.13.0/meta.yaml +++ b/recipes/bam_stats/1.13.0/meta.yaml @@ -21,6 +21,7 @@ source: requirements: build: - {{ compiler("c") }} + - make host: - libhts-dev run: From 847c815a389499f8a0081caaf2d3685febfd0af4 Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 26 Feb 2019 21:35:25 +0000 Subject: [PATCH 060/119] Renamed the openssl sub-package to openssl-bin because of conda/conda-build#3313 Added sub-package requirements to the package root requirements because conda-build does not pick them up from the sub-package definition. Replaced the smoke test with one not requiring to resolve www.sanger.ac.uk. --- recipes/openssl/1.0.2o/meta.yaml | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/recipes/openssl/1.0.2o/meta.yaml b/recipes/openssl/1.0.2o/meta.yaml index 90cde470..68a17d68 100644 --- a/recipes/openssl/1.0.2o/meta.yaml +++ b/recipes/openssl/1.0.2o/meta.yaml @@ -11,15 +11,26 @@ about: summary: "Cryptography and SSL/TLS Toolkit." build: - number: 1 + number: 2 source: - url: https://www.openssl.org/source/openssl-{{ version }}.tar.gz fn: openssl-{{ version }}.tar.gz sha256: {{ sha256 }} +requirements: + build: + - {{ compiler("c") }} + - libtool + - make + - pkg-config + host: + - libz-dev + run: + - libz + outputs: - - name: openssl + - name: openssl-bin version: {{ version }} requirements: build: @@ -38,7 +49,7 @@ outputs: - etc/ssl/man/man1 test: commands: - - openssl s_client -CApath /etc/ssl/certs/ -connect www.sanger.ac.uk:443 + - openssl help - name: libssl version: {{ version }} From f80887f97d270d208c02baf5aed1cd7e82453b64 Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 26 Feb 2019 21:38:51 +0000 Subject: [PATCH 061/119] Do not rename the root package unless we have to. --- recipes/pcre/8.41/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pcre/8.41/meta.yaml b/recipes/pcre/8.41/meta.yaml index 6145b19f..6da72be3 100644 --- a/recipes/pcre/8.41/meta.yaml +++ b/recipes/pcre/8.41/meta.yaml @@ -2,7 +2,7 @@ {% set sha256 = "244838e1f1d14f7e2fa7681b857b3a8566b74215f28133f14a8f5e59241b682c" %} package: - name: pcre-pkg + name: pcre version: "{{ version }}" about: @@ -33,7 +33,7 @@ requirements: - libz outputs: - - name: pcre + - name: pcre-bin version: {{ version }} requirements: build: From 338b63307e9693be1aba51b3cf175b63b942e5d0 Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 26 Feb 2019 21:40:12 +0000 Subject: [PATCH 062/119] Added sub-package requirements to the package root requirements because conda-build does not pick them up from the sub-package definition. Renamed the hdf5 sub-package to hdf5-bin because of conda/conda-build#3313 --- recipes/hdf5/1.10.1/meta.yaml | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/recipes/hdf5/1.10.1/meta.yaml b/recipes/hdf5/1.10.1/meta.yaml index 7a61420b..c28cf5bd 100644 --- a/recipes/hdf5/1.10.1/meta.yaml +++ b/recipes/hdf5/1.10.1/meta.yaml @@ -20,8 +20,17 @@ source: fn: hdf5-{{ version }}.tar.gz sha256: {{ sha256 }} +requirements: + build: + - {{ compiler("cxx") }} + - make + host: + - libz-dev + run: + - libz + outputs: - - name: hdf5 + - name: hdf5-bin version: {{ version }} requirements: build: From 7e04e56f1e8613aca69b976fe47087089725281f Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 26 Feb 2019 21:44:54 +0000 Subject: [PATCH 063/119] Correct sub-package name to be bzip2-bin. --- recipes/bzip2/1.0.6/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/bzip2/1.0.6/meta.yaml b/recipes/bzip2/1.0.6/meta.yaml index 63d83ba2..5c1f86e2 100644 --- a/recipes/bzip2/1.0.6/meta.yaml +++ b/recipes/bzip2/1.0.6/meta.yaml @@ -27,7 +27,7 @@ requirements: - make outputs: - - name: bzip2 + - name: bzip2-bin version: {{ version }} requirements: build: From ee5cca9909a5f30e344c022523286e102e4edcfe Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 26 Feb 2019 21:45:37 +0000 Subject: [PATCH 064/119] Re-enabled --dry-run which was lost by editor-enhanced indent changes. Added printing successful build output when in debug mode. --- scripts/build.py | 35 ++++++++++++++++++----------------- 1 file changed, 18 insertions(+), 17 deletions(-) diff --git a/scripts/build.py b/scripts/build.py index 2ed9279a..b731e19f 100755 --- a/scripts/build.py +++ b/scripts/build.py @@ -132,23 +132,24 @@ def docker_pull(image): log.info('Build script: "%s"', build_script) else: log.debug('Build script: "%s"', build_script) - - try: - subprocess.check_output( - ['docker', 'run', - '--mount', - 'source={},target={},type=bind'.format(args.recipes_dir, - args.recipes_mount), - '--mount', - 'source={},target={},type=bind'.format(args.artefacts_dir, - args.artefacts_mount), - '-i', '-e', 'CONDA_USER_ID=1000', - build_image, - '/bin/sh', '-c', build_script], stderr=subprocess.STDOUT) - except subprocess.CalledProcessError as e: - fail = True - for line in e.output.decode("utf-8").split("\n"): - log.error(line) + try: + output = subprocess.check_output( + ['docker', 'run', + '--mount', + 'source={},target={},type=bind'.format(args.recipes_dir, + args.recipes_mount), + '--mount', + 'source={},target={},type=bind'.format(args.artefacts_dir, + args.artefacts_mount), + '-i', '-e', 'CONDA_USER_ID=1000', + build_image, + '/bin/sh', '-c', build_script], stderr=subprocess.STDOUT) + for line in output.decode("utf-8").split("\n"): + log.debug(line) + except subprocess.CalledProcessError as e: + fail = True + for line in e.output.decode("utf-8").split("\n"): + log.error(line) if fail: exit(1) From 2d3df8fb252874038e7a84df30fd767991a87aea Mon Sep 17 00:00:00 2001 From: Keith James Date: Wed, 27 Feb 2019 16:06:38 +0000 Subject: [PATCH 065/119] Expanded the README. --- README | 2 -- README.md | 64 +++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 64 insertions(+), 2 deletions(-) delete mode 100644 README create mode 100644 README.md diff --git a/README b/README deleted file mode 100644 index dc41ea86..00000000 --- a/README +++ /dev/null @@ -1,2 +0,0 @@ - -Recipes and tools for use with Conda https://conda.io \ No newline at end of file diff --git a/README.md b/README.md new file mode 100644 index 00000000..434338cc --- /dev/null +++ b/README.md @@ -0,0 +1,64 @@ +This repository contains [Conda](https://conda.io) recipes to build +tools and libraries used by [WSI NPG](https://github.com/wtsi-npg). + +Our recipes differ from those provided by +[Anaconda Inc.](https://github.com/AnacondaRecipes), +[Conda Forge](https://conda-forge.org) and +[BioConda](https://bioconda.github.io/) in order to meet our specific +needs: + +* Build artefacts are separated into sub-packages. For a typical + package writen in C and named `example`, these would be: + + * `example-bin` containing executables and their documentation, such + as manpages. + + * `libexample` containing the example libraries (static and shared). + + * `example-dev` containing the C headers, any pkg-config files, + build-time configuration executables and API manpages. + +* Recipes depend only on the Anaconda `defaults` channel + +* We maintain recipes for multiple versions of packages in + production. The recipes are located in directory hierarchy by name + and version. + +* Recipes do not support Windows or MacOS. + +Typical Conda recipes create a single package bundling all build +artefacts (executables, libraries, headers, manpages etc) together, so +installing a program that depends on a C shared library from another +package will cause any executables in that package also to be +installed in the target environment. This is something we specifically +want to avoid. + +We avoid using the `conda-forge` and `bioconda` channels so that we +are in complete control of the deployed package dependency graph and +do not unexpectedly upgrade (or downgrade) packages that may affect +data analysis. + +We don't use the Windows or MacOS platforms, so we simplify our +recipes by omitting support for them. + +### Building the recipes ### + +Building from source requires Conda (we use +[Miniconda](https://docs.conda.io/en/latest/miniconda.html)), with the +[conda-build](https://github.com/conda/conda-build) and +[conda-verify](https://github.com/conda/conda-verify) installed. + +A complete from-source build can be achieved using the +`./scripts/package_sort.py` script which inspects the recipes, +calculates their dependency DAG and then outputs a list sorted so that +they are built in the correct order: + + ./scripts/package_sort.py recipes/ | head -4 + rna-seqc 1.1.8 recipes/rna-seqc/1.1.8 + bowtie2 2.2.7 recipes/bowtie2/2.2.7 + teepot 1.2.0 recipes/teepot/1.2.0 + eigen 3.3.4 recipes/eigen/3.3.4 + +The list of recipe paths may be passed directly to `conda-build`: + + ./scripts/package_sort.py recipes | awk '{print $3}' | xargs conda-build From 3547761b0476ad2d3bd76010ec764d7c28777d85 Mon Sep 17 00:00:00 2001 From: Keith James Date: Wed, 27 Feb 2019 16:12:19 +0000 Subject: [PATCH 066/119] Added clarification on build behaviour. Fixed typos. --- README.md | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 434338cc..e57d7a34 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ Our recipes differ from those provided by needs: * Build artefacts are separated into sub-packages. For a typical - package writen in C and named `example`, these would be: + package written in C and named `example`, these would be: * `example-bin` containing executables and their documentation, such as manpages. @@ -46,7 +46,8 @@ recipes by omitting support for them. Building from source requires Conda (we use [Miniconda](https://docs.conda.io/en/latest/miniconda.html)), with the [conda-build](https://github.com/conda/conda-build) and -[conda-verify](https://github.com/conda/conda-verify) installed. +[conda-verify](https://github.com/conda/conda-verify) packages +installed. A complete from-source build can be achieved using the `./scripts/package_sort.py` script which inspects the recipes, @@ -62,3 +63,6 @@ they are built in the correct order: The list of recipe paths may be passed directly to `conda-build`: ./scripts/package_sort.py recipes | awk '{print $3}' | xargs conda-build + +which will build everything using just the Anaconda defaults channel +and the local channel for dependencies. From 6a6cd72420bb912b6c474cfb584d279ba6294f82 Mon Sep 17 00:00:00 2001 From: Keith James Date: Thu, 28 Feb 2019 10:51:56 +0000 Subject: [PATCH 067/119] Added a --remove-container CLI option to delete the container after each build. Improved the reporting of the --dry-run CLI option. --- scripts/build.py | 35 +++++++++++++++++++++++------------ 1 file changed, 23 insertions(+), 12 deletions(-) diff --git a/scripts/build.py b/scripts/build.py index b731e19f..cd64ba1d 100755 --- a/scripts/build.py +++ b/scripts/build.py @@ -84,6 +84,9 @@ def docker_pull(image): help="Docker image used to build packages, " "defaults to {}".format(DEFAULT_BUILD_IMAGE), type=str, nargs="?", default=DEFAULT_BUILD_IMAGE) +parser.add_argument("--remove-container", + help="Remove the Docker container after each build", + action="store_true") parser.add_argument("--dry-run", help="Log the recipes that would be built at INFO level, " @@ -128,22 +131,30 @@ def docker_pull(image): CONDA_CHANNEL, args.recipes_mount, path) + run_cmd = ['docker', 'run'] + mount_args = ['--mount', + 'source={},target={},type=bind'.format(args.recipes_dir, + args.recipes_mount), + '--mount', + 'source={},target={},type=bind'.format(args.artefacts_dir, + args.artefacts_mount)] + env_args = ['-e', 'CONDA_USER_ID=1000'] + other_args = ['-i'] + script_args = ['/bin/sh', '-c', build_script] + + if args.remove_container: + other_args.append('--rm') + + cmd = run_cmd + mount_args + env_args + other_args + [build_image] \ + + script_args + if args.dry_run: - log.info('Build script: "%s"', build_script) + log.info('Docker command: "%s"', cmd) else: log.debug('Build script: "%s"', build_script) + try: - output = subprocess.check_output( - ['docker', 'run', - '--mount', - 'source={},target={},type=bind'.format(args.recipes_dir, - args.recipes_mount), - '--mount', - 'source={},target={},type=bind'.format(args.artefacts_dir, - args.artefacts_mount), - '-i', '-e', 'CONDA_USER_ID=1000', - build_image, - '/bin/sh', '-c', build_script], stderr=subprocess.STDOUT) + output = subprocess.check_output(cmd, stderr=subprocess.STDOUT) for line in output.decode("utf-8").split("\n"): log.debug(line) except subprocess.CalledProcessError as e: From 755bf2b6f20f9470b339c232f2d02e637da99909 Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 4 Mar 2019 14:11:56 +0000 Subject: [PATCH 068/119] Link against Conda OpenSSL library, rather than the system one, for portability. --- recipes/irods/4.1.12/build.sh | 6 +++++- recipes/irods/4.1.12/meta.yaml | 14 +++++++++++++- 2 files changed, 18 insertions(+), 2 deletions(-) diff --git a/recipes/irods/4.1.12/build.sh b/recipes/irods/4.1.12/build.sh index 2b21ee77..28c92e02 100644 --- a/recipes/irods/4.1.12/build.sh +++ b/recipes/irods/4.1.12/build.sh @@ -88,7 +88,9 @@ if [ -f /etc/lsb-release ]; then install_gcc_ubuntu install_deps_ubuntu fi - + + export CCFLAGS="-I$PREFIX/include" + export LDRFLAGS="-L$PREFIX/lib" ./packaging/build.sh --verbose icat postgres ./packaging/build.sh --verbose icommands @@ -109,6 +111,8 @@ if [ -f /etc/redhat-release ]; then install_deps_rhel fi + export CCFLAGS="$PREFIX/include" + export LDRFLAGS="$PREFIX/lib" ./packaging/build.sh --verbose icat postgres ./packaging/build.sh --verbose icommands diff --git a/recipes/irods/4.1.12/meta.yaml b/recipes/irods/4.1.12/meta.yaml index 216bf965..b55379b8 100644 --- a/recipes/irods/4.1.12/meta.yaml +++ b/recipes/irods/4.1.12/meta.yaml @@ -10,15 +10,26 @@ about: summary: "Open Source Data Management Software." build: - number: 2 + number: 3 source: git_url: https://github.com/irods/irods.git git_rev: 4-1-stable +requirements: + host: + - libssl-dev + run: + - libssl + outputs: - name: irods-plugins version: {{ version }} + requirements: + host: + - libssl-dev + run: + - libssl files: - lib/irods/plugins @@ -44,6 +55,7 @@ outputs: requirements: run: - {{ pin_subpackage("irods-plugins", exact=True) }} + - libssl files: - bin/iadmin - bin/ibun From f06380400e65d2013522cfb66a8cd256141cf6b7 Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 5 Mar 2019 09:47:50 +0000 Subject: [PATCH 069/119] Added a top-level conda_build_config.yaml to set -march and -mtune. Tidied other conda_build_config.yaml files. --- conda_build_config.yaml | 11 +++++++++++ recipes/bowtie/1.2.2/conda_build_config.yaml | 12 +++++++++++- recipes/tophat2/2.1.1/conda_build_config.yaml | 1 - 3 files changed, 22 insertions(+), 2 deletions(-) create mode 100644 conda_build_config.yaml diff --git a/conda_build_config.yaml b/conda_build_config.yaml new file mode 100644 index 00000000..05b510b9 --- /dev/null +++ b/conda_build_config.yaml @@ -0,0 +1,11 @@ + +CFLAGS: > + -O2 + -fPIC + -ffunction-sections + -fno-plt + -fstack-protector-strong + -ftree-vectorize + -march=x86-64 + -mtune=generic + -pipe diff --git a/recipes/bowtie/1.2.2/conda_build_config.yaml b/recipes/bowtie/1.2.2/conda_build_config.yaml index bd154b47..615d1db9 100644 --- a/recipes/bowtie/1.2.2/conda_build_config.yaml +++ b/recipes/bowtie/1.2.2/conda_build_config.yaml @@ -1,3 +1,13 @@ # Set -std=c++03 (see https://github.com/BenLangmead/bowtie/issues/76) -CXXFLAGS: "-march=x86-64 -mtune=generic -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -std=c++03" +CXXFLAGS: > + -O2 + -fPIC + -ffunction-sections + -fno-plt + -fstack-protector-strong + -ftree-vectorize + -march=x86-64 + -mtune=generic + -pipe + -std=c++03 diff --git a/recipes/tophat2/2.1.1/conda_build_config.yaml b/recipes/tophat2/2.1.1/conda_build_config.yaml index 15150c0f..54d7f516 100644 --- a/recipes/tophat2/2.1.1/conda_build_config.yaml +++ b/recipes/tophat2/2.1.1/conda_build_config.yaml @@ -3,4 +3,3 @@ c_compiler_version: cxx_compiler_version: - 5.4 - From f83d454993cd0c86edd6d99cd7d584013a309758 Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 5 Mar 2019 10:42:47 +0000 Subject: [PATCH 070/119] GCC 5.4 doesn't support -fno-plt, so override the CFLAGS stet the root conda_build_config.yaml --- recipes/boost/1.68.0/conda_build_config.yaml | 10 ++++++++++ .../fastx_toolkit/0.0.14/conda_build_config.yaml | 10 ++++++++++ recipes/irods/4.1.12/conda_build_config.yaml | 15 +++++++++------ recipes/tophat2/2.1.1/conda_build_config.yaml | 10 ++++++++++ recipes/verifybamid/1.1.3/conda_build_config.yaml | 10 ++++++++++ 5 files changed, 49 insertions(+), 6 deletions(-) diff --git a/recipes/boost/1.68.0/conda_build_config.yaml b/recipes/boost/1.68.0/conda_build_config.yaml index 54d7f516..b7c16dfe 100644 --- a/recipes/boost/1.68.0/conda_build_config.yaml +++ b/recipes/boost/1.68.0/conda_build_config.yaml @@ -3,3 +3,13 @@ c_compiler_version: cxx_compiler_version: - 5.4 + +CFLAGS: > + -O2 + -fPIC + -ffunction-sections + -fstack-protector-strong + -ftree-vectorize + -march=x86-64 + -mtune=generic + -pipe diff --git a/recipes/fastx_toolkit/0.0.14/conda_build_config.yaml b/recipes/fastx_toolkit/0.0.14/conda_build_config.yaml index 54d7f516..b7c16dfe 100644 --- a/recipes/fastx_toolkit/0.0.14/conda_build_config.yaml +++ b/recipes/fastx_toolkit/0.0.14/conda_build_config.yaml @@ -3,3 +3,13 @@ c_compiler_version: cxx_compiler_version: - 5.4 + +CFLAGS: > + -O2 + -fPIC + -ffunction-sections + -fstack-protector-strong + -ftree-vectorize + -march=x86-64 + -mtune=generic + -pipe diff --git a/recipes/irods/4.1.12/conda_build_config.yaml b/recipes/irods/4.1.12/conda_build_config.yaml index 15150c0f..53574ef5 100644 --- a/recipes/irods/4.1.12/conda_build_config.yaml +++ b/recipes/irods/4.1.12/conda_build_config.yaml @@ -1,6 +1,9 @@ -c_compiler_version: - - 5.4 - -cxx_compiler_version: - - 5.4 - +CFLAGS: > + -O2 + -fPIC + -ffunction-sections + -fstack-protector-strong + -ftree-vectorize + -march=x86-64 + -mtune=generic + -pipe diff --git a/recipes/tophat2/2.1.1/conda_build_config.yaml b/recipes/tophat2/2.1.1/conda_build_config.yaml index 54d7f516..b7c16dfe 100644 --- a/recipes/tophat2/2.1.1/conda_build_config.yaml +++ b/recipes/tophat2/2.1.1/conda_build_config.yaml @@ -3,3 +3,13 @@ c_compiler_version: cxx_compiler_version: - 5.4 + +CFLAGS: > + -O2 + -fPIC + -ffunction-sections + -fstack-protector-strong + -ftree-vectorize + -march=x86-64 + -mtune=generic + -pipe diff --git a/recipes/verifybamid/1.1.3/conda_build_config.yaml b/recipes/verifybamid/1.1.3/conda_build_config.yaml index 54d7f516..b7c16dfe 100644 --- a/recipes/verifybamid/1.1.3/conda_build_config.yaml +++ b/recipes/verifybamid/1.1.3/conda_build_config.yaml @@ -3,3 +3,13 @@ c_compiler_version: cxx_compiler_version: - 5.4 + +CFLAGS: > + -O2 + -fPIC + -ffunction-sections + -fstack-protector-strong + -ftree-vectorize + -march=x86-64 + -mtune=generic + -pipe From fa058a794ea571fbeed4e813612a05e111daa4db Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 5 Mar 2019 11:34:06 +0000 Subject: [PATCH 071/119] iRODS compiler does not accept -fstack-protector-strong. Add a chomp operator to build config CFLAGS. --- conda_build_config.yaml | 2 +- recipes/boost/1.68.0/conda_build_config.yaml | 2 +- recipes/bowtie/1.2.2/conda_build_config.yaml | 2 +- recipes/fastx_toolkit/0.0.14/conda_build_config.yaml | 2 +- recipes/irods/4.1.12/conda_build_config.yaml | 4 ++-- recipes/tophat2/2.1.1/conda_build_config.yaml | 2 +- recipes/verifybamid/1.1.3/conda_build_config.yaml | 2 +- 7 files changed, 8 insertions(+), 8 deletions(-) diff --git a/conda_build_config.yaml b/conda_build_config.yaml index 05b510b9..0c61ff42 100644 --- a/conda_build_config.yaml +++ b/conda_build_config.yaml @@ -1,5 +1,5 @@ -CFLAGS: > +CFLAGS: >- -O2 -fPIC -ffunction-sections diff --git a/recipes/boost/1.68.0/conda_build_config.yaml b/recipes/boost/1.68.0/conda_build_config.yaml index b7c16dfe..e1df0f87 100644 --- a/recipes/boost/1.68.0/conda_build_config.yaml +++ b/recipes/boost/1.68.0/conda_build_config.yaml @@ -4,7 +4,7 @@ c_compiler_version: cxx_compiler_version: - 5.4 -CFLAGS: > +CFLAGS: >- -O2 -fPIC -ffunction-sections diff --git a/recipes/bowtie/1.2.2/conda_build_config.yaml b/recipes/bowtie/1.2.2/conda_build_config.yaml index 615d1db9..ed7751d4 100644 --- a/recipes/bowtie/1.2.2/conda_build_config.yaml +++ b/recipes/bowtie/1.2.2/conda_build_config.yaml @@ -1,6 +1,6 @@ # Set -std=c++03 (see https://github.com/BenLangmead/bowtie/issues/76) -CXXFLAGS: > +CXXFLAGS: >- -O2 -fPIC -ffunction-sections diff --git a/recipes/fastx_toolkit/0.0.14/conda_build_config.yaml b/recipes/fastx_toolkit/0.0.14/conda_build_config.yaml index b7c16dfe..e1df0f87 100644 --- a/recipes/fastx_toolkit/0.0.14/conda_build_config.yaml +++ b/recipes/fastx_toolkit/0.0.14/conda_build_config.yaml @@ -4,7 +4,7 @@ c_compiler_version: cxx_compiler_version: - 5.4 -CFLAGS: > +CFLAGS: >- -O2 -fPIC -ffunction-sections diff --git a/recipes/irods/4.1.12/conda_build_config.yaml b/recipes/irods/4.1.12/conda_build_config.yaml index 53574ef5..d787178a 100644 --- a/recipes/irods/4.1.12/conda_build_config.yaml +++ b/recipes/irods/4.1.12/conda_build_config.yaml @@ -1,8 +1,8 @@ -CFLAGS: > + +CFLAGS: >- -O2 -fPIC -ffunction-sections - -fstack-protector-strong -ftree-vectorize -march=x86-64 -mtune=generic diff --git a/recipes/tophat2/2.1.1/conda_build_config.yaml b/recipes/tophat2/2.1.1/conda_build_config.yaml index b7c16dfe..e1df0f87 100644 --- a/recipes/tophat2/2.1.1/conda_build_config.yaml +++ b/recipes/tophat2/2.1.1/conda_build_config.yaml @@ -4,7 +4,7 @@ c_compiler_version: cxx_compiler_version: - 5.4 -CFLAGS: > +CFLAGS: >- -O2 -fPIC -ffunction-sections diff --git a/recipes/verifybamid/1.1.3/conda_build_config.yaml b/recipes/verifybamid/1.1.3/conda_build_config.yaml index b7c16dfe..e1df0f87 100644 --- a/recipes/verifybamid/1.1.3/conda_build_config.yaml +++ b/recipes/verifybamid/1.1.3/conda_build_config.yaml @@ -4,7 +4,7 @@ c_compiler_version: cxx_compiler_version: - 5.4 -CFLAGS: > +CFLAGS: >- -O2 -fPIC -ffunction-sections From b1decad1b6b7f2aae7cf03503abcecfc13cd9203 Mon Sep 17 00:00:00 2001 From: Kevin Lewis Date: Wed, 6 Mar 2019 15:18:23 +0000 Subject: [PATCH 072/119] bambi 0.12.0 --- recipes/bambi/0.12.0/build.sh | 12 ++++++++++++ recipes/bambi/0.12.0/meta.yaml | 35 ++++++++++++++++++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100755 recipes/bambi/0.12.0/build.sh create mode 100644 recipes/bambi/0.12.0/meta.yaml diff --git a/recipes/bambi/0.12.0/build.sh b/recipes/bambi/0.12.0/build.sh new file mode 100755 index 00000000..1a1c597a --- /dev/null +++ b/recipes/bambi/0.12.0/build.sh @@ -0,0 +1,12 @@ +#!/bin/sh + +set -e + +autoreconf -fi + +n=`expr $CPU_COUNT / 4 \| 1` + +./configure --prefix="$PREFIX" --with-htslib="$PREFIX" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" + +make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make install prefix="$PREFIX" diff --git a/recipes/bambi/0.12.0/meta.yaml b/recipes/bambi/0.12.0/meta.yaml new file mode 100644 index 00000000..bc419bfd --- /dev/null +++ b/recipes/bambi/0.12.0/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.12.0" %} +{% set htslib_version = "1.9" %} + + +package: + name: bambi + version: "{{ version }}" + +about: + home: https://github.com/wtsi-npg/bambi + license: AGPL + summary: "A set of programs to manipulate SAM/BAM/CRAM files, using HTSLIB." + +build: + number: 0 + +source: + git_url: https://github.com/wtsi-npg/bambi.git + git_rev: 0.12.0 + +requirements: + build: + - gcc_npg >=7.3 + - htslib =={{ htslib_version }} + - libgd + - libxml2 + + run: + - htslib >={{ htslib_version }} + - libgd + - libxml2 + +test: + commands: + - bambi --version From b83f88dfae04b30263bdd2f84210f8e5486a3a27 Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 11 Mar 2019 09:01:45 +0000 Subject: [PATCH 073/119] Disable -O2 for iRODS as a workaround to prevent the GLIBC symbol __fdelt_chk being required by libRodsAPIs.a which is not present in the Conda glibc. --- recipes/irods/4.1.12/conda_build_config.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/recipes/irods/4.1.12/conda_build_config.yaml b/recipes/irods/4.1.12/conda_build_config.yaml index d787178a..6459c5db 100644 --- a/recipes/irods/4.1.12/conda_build_config.yaml +++ b/recipes/irods/4.1.12/conda_build_config.yaml @@ -1,6 +1,5 @@ CFLAGS: >- - -O2 -fPIC -ffunction-sections -ftree-vectorize From 3f83d37a5dc71f716214e02e7a9312805a714abb Mon Sep 17 00:00:00 2001 From: Keith James Date: Wed, 13 Mar 2019 12:36:58 +0000 Subject: [PATCH 074/119] Corrected build.py validation rule to 'URI'. Added --build-channel CLI option. Added a dependency on Python rfc3987 to validate URL arguments supplied to --build-channel. Updated the default Docker images used to run builds. --- .travis.yml | 11 +++++++---- scripts/build.py | 38 +++++++++++++++++++++++++++----------- 2 files changed, 34 insertions(+), 15 deletions(-) diff --git a/.travis.yml b/.travis.yml index ff51711e..0dba94d4 100644 --- a/.travis.yml +++ b/.travis.yml @@ -7,8 +7,9 @@ services: docker env: - > - IRODS_IMAGE=wsinpg/conda-irods-12.04:0.2 - CONDA_IMAGE=wsinpg/conda-12.04:0.2 + IRODS_IMAGE=wsinpg/ub-12.04-conda-irods-4.1:0.3 + CONDA_IMAGE=wsinpg/ub-12.04-conda:0.3 + CONDA_CHANNEL=https://dnap.cog.sanger.ac.uk/npg/conda/devel/generic COMPARE_BRANCH=origin/devel before_install: @@ -18,7 +19,7 @@ before_install: - docker pull $CONDA_IMAGE install: - - pip install jinja2 networkx packaging pyaml setuptools + - pip install jinja2 networkx packaging pyaml rfc3987 setuptools # Ensure we have a complete repository to compare diffs with other # branches - git config remote.origin.fetch +refs/heads/*:refs/remotes/origin/* @@ -32,6 +33,8 @@ script: --recipes-dir $TRAVIS_BUILD_DIR --artefacts-dir $TRAVIS_BUILD_DIR/conda-artefacts --irods-build-image $IRODS_IMAGE - --conda-build-image $CONDA_IMAGE --verbose + --conda-build-image $CONDA_IMAGE + --build-channel $CONDA_CHANNEL + --verbose - kill %1 - ls -l $TRAVIS_BUILD_DIR/conda-artefacts/linux-64 diff --git a/scripts/build.py b/scripts/build.py index cd64ba1d..6838ce6b 100755 --- a/scripts/build.py +++ b/scripts/build.py @@ -25,6 +25,7 @@ import subprocess import time +import rfc3987 def docker_pull(image): subprocess.check_output(['docker', 'pull', image]) @@ -36,10 +37,8 @@ def docker_pull(image): DEFAULT_ARTEFACTS_DIR=os.path.expandvars("$HOME/conda-artefacts") DEFAULT_ARTEFACTS_MOUNT="/opt/conda/conda-bld" -IRODS_BUILD_IMAGE="wsinpg/conda-irods-12.04:0.2" -DEFAULT_BUILD_IMAGE="wsinpg/conda-12.04:0.2" - -CONDA_CHANNEL="https://dnap.cog.sanger.ac.uk/npg/conda/devel/" +IRODS_BUILD_IMAGE="wsinpg/ub-12.04-conda-irods:0.3" +DEFAULT_BUILD_IMAGE="wsinpg/ub-12.04-conda:0.3" description = """ @@ -76,6 +75,12 @@ def docker_pull(image): "defaults to {}".format(DEFAULT_ARTEFACTS_MOUNT), type=str, nargs="?", default=DEFAULT_ARTEFACTS_MOUNT) +parser.add_argument("--build-channel", + help="The Conda channel from which to get dependencies " + "when not doing a full, local from-source build, " + "defaults to none (forcing a local build)", + type=str, nargs="?", default=None) + parser.add_argument("--irods-build-image", help="The Docker image used to build iRODS, " "defaults to {}".format(IRODS_BUILD_IMAGE), @@ -108,6 +113,13 @@ def docker_pull(image): level = log.INFO log.basicConfig(level=level) +if args.build_channel: + try: + rfc3987.parse(args.build_channel, rule='URI') + except ValueError as e: + log.error("Invalid --build-channel URL '%s'", args.build_channel) + exit(1) + docker_pull(args.conda_build_image) fail = False @@ -124,13 +136,17 @@ def docker_pull(image): docker_pull(args.irods_build_image) build_script = \ - 'export CONDA_BLD_PATH="{}" ; ' \ - 'conda config --set auto_update_conda False ; ' \ - 'conda config --add channels {} ; ' \ - 'cd "{}" && conda build {}'.format(args.artefacts_mount, - CONDA_CHANNEL, - args.recipes_mount, - path) + 'export CONDA_BLD_PATH="{}" ; '.format(args.artefacts_mount) + build_script += \ + 'conda config --set auto_update_conda False ; ' + + if args.build_channel: + build_script += \ + 'conda config --add channels {} ; '.format(args.build_channel) + + build_script += \ + 'cd "{}" && conda build {}'.format(args.recipes_mount, path) + run_cmd = ['docker', 'run'] mount_args = ['--mount', 'source={},target={},type=bind'.format(args.recipes_dir, From ff82d5e21a661fb3d03ca13c40d54a3cde488990 Mon Sep 17 00:00:00 2001 From: Kevin Lewis Date: Wed, 27 Mar 2019 13:58:45 +0000 Subject: [PATCH 075/119] Update meta.yaml --- recipes/bambi/0.12.0/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bambi/0.12.0/meta.yaml b/recipes/bambi/0.12.0/meta.yaml index bc419bfd..5c8bae42 100644 --- a/recipes/bambi/0.12.0/meta.yaml +++ b/recipes/bambi/0.12.0/meta.yaml @@ -1,5 +1,5 @@ {% set version = "0.12.0" %} -{% set htslib_version = "1.9" %} +{% set htslib_version = "1.9+66_gbcf9bff" %} package: @@ -26,7 +26,7 @@ requirements: - libxml2 run: - - htslib >={{ htslib_version }} + - htslib =={{ htslib_version }} - libgd - libxml2 From b033e0b267f83424e0c0d30bc01e4a1cc396e87c Mon Sep 17 00:00:00 2001 From: Keith James Date: Wed, 27 Mar 2019 16:17:55 +0000 Subject: [PATCH 076/119] Added libdeflate 1.2 and updated the htslib build to use it. --- recipes/htslib/1.9+66-gbcf9bff/build.sh | 19 +++++++------ recipes/htslib/1.9+66-gbcf9bff/meta.yaml | 7 +++-- recipes/libdeflate/1.2/build.sh | 8 ++++++ recipes/libdeflate/1.2/meta.yaml | 36 ++++++++++++++++++++++++ 4 files changed, 60 insertions(+), 10 deletions(-) create mode 100644 recipes/libdeflate/1.2/build.sh create mode 100644 recipes/libdeflate/1.2/meta.yaml diff --git a/recipes/htslib/1.9+66-gbcf9bff/build.sh b/recipes/htslib/1.9+66-gbcf9bff/build.sh index 45df1b01..411e5319 100755 --- a/recipes/htslib/1.9+66-gbcf9bff/build.sh +++ b/recipes/htslib/1.9+66-gbcf9bff/build.sh @@ -1,6 +1,6 @@ #!/bin/sh -set -e +set -ex n=`expr $CPU_COUNT / 4 \| 1` @@ -10,15 +10,18 @@ cp aclocal.m4 aclocal.m4.tmp autoreconf cp aclocal.m4.tmp aclocal.m4 -./configure --prefix="$PREFIX" \ - --enable-libcurl \ - --enable-plugins \ - CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make -j $n +CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" \ + ./configure --prefix="$PREFIX" \ + --enable-libcurl \ + --enable-libdeflate \ + --enable-plugins \ + +make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install prefix="$PREFIX" popd pushd plugins -make install prefix="$PREFIX" IRODS_HOME="$PREFIX" \ - CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" \ + IRODS_HOME="$PREFIX" +make install prefix="$PREFIX" popd diff --git a/recipes/htslib/1.9+66-gbcf9bff/meta.yaml b/recipes/htslib/1.9+66-gbcf9bff/meta.yaml index e5679735..b3bc6526 100644 --- a/recipes/htslib/1.9+66-gbcf9bff/meta.yaml +++ b/recipes/htslib/1.9+66-gbcf9bff/meta.yaml @@ -12,7 +12,7 @@ about: summary: C library for high-throughput sequencing data formats. build: - number: 0 + number: 1 string: plugins_{{ plugins_rev }}_{{ PKG_BUILDNUM }} source: @@ -30,12 +30,13 @@ requirements: build: - libbzip2 - libcurl + - libdeflate - gcc_npg >=7.3 - irods-dev >=4.1.12 # for plugins - liblzma - openssl - zlib - + outputs: - name: htsbin version: {{ version }} @@ -44,6 +45,7 @@ outputs: - htslib =={{ version }} - libbzip2 - libcurl + - libdeflate - liblzma - openssl - zlib @@ -60,6 +62,7 @@ outputs: run: - libbzip2 - libcurl + - libdeflate - liblzma - openssl - zlib diff --git a/recipes/libdeflate/1.2/build.sh b/recipes/libdeflate/1.2/build.sh new file mode 100644 index 00000000..d6f70511 --- /dev/null +++ b/recipes/libdeflate/1.2/build.sh @@ -0,0 +1,8 @@ +#!/bin/sh + +set -ex + +n="$CPU_COUNT" + +make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make install prefix="$PREFIX" diff --git a/recipes/libdeflate/1.2/meta.yaml b/recipes/libdeflate/1.2/meta.yaml new file mode 100644 index 00000000..b6d1fd3f --- /dev/null +++ b/recipes/libdeflate/1.2/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.2" %} +{% set sha256 = "d30203c3a2fae6cee70d52a59cc668740f806a4bb9eb6668930fb7de99464d90" %} + +package: + name: libdeflate-pkg + version: "{{ version }}" + +about: + home: https://github.com/ebiggers/libdeflate + license: MIT + summary: >- + Heavily optimized library for DEFLATE/zlib/gzip compression and + decompression. + +source: + url: https://github.com/ebiggers/libdeflate/archive/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - gcc_npg >=7.3 + +outputs: + - name: libdeflate + files: + - include/libdeflate.h + - lib/libdeflate* + +test: + commands: + - test -f ${PREFIX}/include/libdeflate.h + - test -f ${PREFIX}/lib/libdeflate.a + - test -h ${PREFIX}/lib/libdeflate.so From 040b416a1990304d9bbdb89dde45cec13821e7eb Mon Sep 17 00:00:00 2001 From: Keith James Date: Thu, 28 Mar 2019 11:47:38 +0000 Subject: [PATCH 077/119] Use gcc old enough to be compatible with the kernel and binutils (e.g. prevents generation of unsupported AVX instructions on Skylake). --- recipes/libdeflate/1.2/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/libdeflate/1.2/meta.yaml b/recipes/libdeflate/1.2/meta.yaml index b6d1fd3f..70cd43fc 100644 --- a/recipes/libdeflate/1.2/meta.yaml +++ b/recipes/libdeflate/1.2/meta.yaml @@ -21,7 +21,7 @@ build: requirements: build: - - gcc_npg >=7.3 + - gcc_npg <5.0 outputs: - name: libdeflate From 7966d0bc27b4203009060c3b06031e7955eb3ecf Mon Sep 17 00:00:00 2001 From: Keith James Date: Thu, 28 Mar 2019 11:57:16 +0000 Subject: [PATCH 078/119] Change the gcc version to one that is old enough AND that we have build for both Precise and Bionic. --- recipes/libdeflate/1.2/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/libdeflate/1.2/meta.yaml b/recipes/libdeflate/1.2/meta.yaml index 70cd43fc..d61e3f43 100644 --- a/recipes/libdeflate/1.2/meta.yaml +++ b/recipes/libdeflate/1.2/meta.yaml @@ -21,7 +21,7 @@ build: requirements: build: - - gcc_npg <5.0 + - gcc_npg ==5.5 outputs: - name: libdeflate From b723e7e045f6ce779ae993b03293e87b4f44f0ec Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 1 Apr 2019 10:53:17 +0100 Subject: [PATCH 079/119] Removed extra whitespace. --- recipes/htslib/1.9+66-gbcf9bff/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/htslib/1.9+66-gbcf9bff/meta.yaml b/recipes/htslib/1.9+66-gbcf9bff/meta.yaml index b3bc6526..fae2772d 100644 --- a/recipes/htslib/1.9+66-gbcf9bff/meta.yaml +++ b/recipes/htslib/1.9+66-gbcf9bff/meta.yaml @@ -36,7 +36,7 @@ requirements: - liblzma - openssl - zlib - + outputs: - name: htsbin version: {{ version }} From 4837546a05e52cd2a12597b2de3123db2faa96fb Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 8 Apr 2019 15:36:05 +0100 Subject: [PATCH 080/119] Added babmboi 0.12.0 Added htslib 1.9+66_gbcf9bff --- recipes/bambi/0.12.0/build.sh | 13 +++ recipes/bambi/0.12.0/meta.yaml | 41 ++++++++ recipes/htslib/1.9+66_gbcf9bff/build.sh | 27 +++++ recipes/htslib/1.9+66_gbcf9bff/meta.yaml | 125 +++++++++++++++++++++++ 4 files changed, 206 insertions(+) create mode 100755 recipes/bambi/0.12.0/build.sh create mode 100644 recipes/bambi/0.12.0/meta.yaml create mode 100755 recipes/htslib/1.9+66_gbcf9bff/build.sh create mode 100644 recipes/htslib/1.9+66_gbcf9bff/meta.yaml diff --git a/recipes/bambi/0.12.0/build.sh b/recipes/bambi/0.12.0/build.sh new file mode 100755 index 00000000..0deb559a --- /dev/null +++ b/recipes/bambi/0.12.0/build.sh @@ -0,0 +1,13 @@ +#!/bin/sh + +set -ex + +autoreconf -fi + +n="$CPU_COUNT" + +CPPFLAGS="-I$PREFIX/include" LDFLAGS="-Wl,-rpath,$PREFIX/lib -L$PREFIX/lib" \ + ./configure --prefix="$PREFIX" --with-htslib="$PREFIX" + +make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make install prefix="$PREFIX" diff --git a/recipes/bambi/0.12.0/meta.yaml b/recipes/bambi/0.12.0/meta.yaml new file mode 100644 index 00000000..bd408678 --- /dev/null +++ b/recipes/bambi/0.12.0/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "0.12.0" %} +{% set htslib_version = "1.9+66_gbcf9bff" %} + +package: + name: bambi + version: "{{ version }}" + +about: + home: https://github.com/wtsi-npg/bambi + license: AGPL + summary: "A set of programs to manipulate SAM/BAM/CRAM files, using HTSLIB." + +build: + number: 0 + +source: + git_url: https://github.com/wtsi-npg/bambi.git + git_rev: 0.12.0 + +requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + - pkg-config + host: + - libgd-dev + - libhts-dev =={{ htslib_version }} + - libxml2-dev + - libz-dev + run: + - libgd + - libhts =={{ htslib_version }} + - libxml2 + - libz + +test: + commands: + - bambi --version diff --git a/recipes/htslib/1.9+66_gbcf9bff/build.sh b/recipes/htslib/1.9+66_gbcf9bff/build.sh new file mode 100755 index 00000000..612cdad2 --- /dev/null +++ b/recipes/htslib/1.9+66_gbcf9bff/build.sh @@ -0,0 +1,27 @@ +#!/bin/sh + +set -ex + +n="$CPU_COUNT" + +pushd htslib + +cp aclocal.m4 aclocal.m4.tmp +autoreconf +cp aclocal.m4.tmp aclocal.m4 + +CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" \ + ./configure --prefix="$PREFIX" \ + --enable-libcurl \ + --enable-plugins + +make -j $n AR="$AR" CC="$GCC" \ + CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make install prefix="$PREFIX" +popd + +pushd plugins +make IRODS_HOME="$PREFIX" \ + CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make install prefix="$PREFIX" +popd diff --git a/recipes/htslib/1.9+66_gbcf9bff/meta.yaml b/recipes/htslib/1.9+66_gbcf9bff/meta.yaml new file mode 100644 index 00000000..21e932fa --- /dev/null +++ b/recipes/htslib/1.9+66_gbcf9bff/meta.yaml @@ -0,0 +1,125 @@ +{% set version = "1.9+66_gbcf9bff" %} +{% set plugins_rev = "201712" %} +{% set htslib_rev = "bcf9bff178f81c9c1cf3a052aeb6cbe32fe5fdcc" %} + +package: + name: "htslib" + version: "{{ version }}" + +about: + home: https://github.com/samtools/htslib + license: MIT + summary: C library for high-throughput sequencing data formats. + +build: + number: 1 + string: plugins_{{ plugins_rev }}_{{ PKG_BUILDNUM }} + +source: + - git_url: https://github.com/samtools/htslib.git + git_rev: {{ htslib_rev }} + folder: htslib + - git_url: https://github.com/samtools/htslib-plugins.git + git_rev: {{ plugins_rev }} + folder: plugins + +features: + - irods + +requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - irods-dev >=4.1.12 + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libssl-dev + - libz-dev + run: + - libbz2 + - libcurl + - liblzma + - libssl + - libz + +outputs: + - name: htslib-bin + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - irods-dev >=4.1.12 + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libssl-dev + - libz-dev + run: + - {{ pin_subpackage("libhts", exact=True) }} + - libbz2 + - libcurl + - liblzma + - libssl + - libz + files: + - bin/bgzip + - bin/htsfile + - bin/tabix + - share/man/man1/htsfile.1 + - share/man/man1/tabix.1 + + - name: libhts + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - irods-dev >=4.1.12 + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libssl-dev + - libz-dev + run: + - libbz2 + - libcurl + - liblzma + - libssl + - libz + files: + - libexec/htslib + - lib/libhts* + test: + commands: + - test -f ${PREFIX}/lib/libhts.a + - test -h ${PREFIX}/lib/libhts.so + - test -f ${PREFIX}/libexec/htslib/hfile_irods.so + - test -f ${PREFIX}/libexec/htslib/hfile_libcurl.so + + - name: libhts-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libhts", exact=True) }} + files: + - include/htslib + - share/man/man5/faidx.5 + - share/man/man5/sam.5 + - share/man/man5/vcf.5 + test: + commands: + - test -f ${PREFIX}/include/htslib/sam.h From 351a8a8895e8e718afe878832d9a6d6b129a846c Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Fri, 12 Apr 2019 16:35:13 +0100 Subject: [PATCH 081/119] wr 0.18.0 --- recipes/wr/0.18.0/build.sh | 12 ++++++++++++ recipes/wr/0.18.0/meta.yaml | 24 ++++++++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 recipes/wr/0.18.0/build.sh create mode 100644 recipes/wr/0.18.0/meta.yaml diff --git a/recipes/wr/0.18.0/build.sh b/recipes/wr/0.18.0/build.sh new file mode 100644 index 00000000..f093a2c3 --- /dev/null +++ b/recipes/wr/0.18.0/build.sh @@ -0,0 +1,12 @@ +#!/bin/sh + +set -e + +mkdir -p "$PREFIX/bin" +cp wr "$PREFIX/bin/" + +mkdir -p "$PREFIX/etc" +cp wr_config.yml "$PREFIX/etc/" + +mkdir -p "$PREFIX/share/doc/wr" +cp README.md "$PREFIX/share/doc/wr/" diff --git a/recipes/wr/0.18.0/meta.yaml b/recipes/wr/0.18.0/meta.yaml new file mode 100644 index 00000000..b9349713 --- /dev/null +++ b/recipes/wr/0.18.0/meta.yaml @@ -0,0 +1,24 @@ +{% set version = "0.18.0" %} +{% set sha256 = "4e02580364635cefdc6c0f3d1a8b63ed3b5d6b103677cd907e5491c683614de2" %} + +package: + name: wr + version: "{{ version }}" + +about: + home: https://github.com/VertebrateResequencing/wr + license: GPLv3 + summary: "High performance Workflow Runner." + +build: + number: 0 + binary_relocation: false + +source: + url: https://github.com/VertebrateResequencing/wr/releases/download/v{{ version }}/wr-linux-x86-64.zip + fn: wr-{{ version }}.zip + sha256: {{ sha256 }} + +test: + commands: + - wr -h From 2b8c5135e5be72adef381093df6836da9f4e1999 Mon Sep 17 00:00:00 2001 From: Keith James Date: Fri, 3 May 2019 09:51:24 +0100 Subject: [PATCH 082/119] Ensure that many changes made to CPPFLAGS and LDFLAGS by configure are preserved when calling make. This is particularly important for htslib where this caused a bug. The successfully built package was unable to locate the htslib plugins at runtime because that information was set by configure in CPPFLAGS. --- recipes/baton/1.1.0/build.sh | 11 +++++------ recipes/bowtie2/2.2.7/build.sh | 3 ++- recipes/fastx_toolkit/0.0.14/build.sh | 4 ++-- recipes/htslib/1.9+47-gc93b673/build.sh | 12 ++++++------ recipes/htslib/1.9+66_gbcf9bff/build.sh | 12 ++++++------ recipes/htslib/1.9+9-g6ec3b94/build.sh | 14 +++++++------- recipes/jansson/2.1.0/build.sh | 5 ++--- recipes/jq/1.5/build.sh | 2 +- recipes/libgd/2.2.5/build.sh | 5 +++-- recipes/libpng/1.6.34/build.sh | 2 +- recipes/samtools/1.9+2-g02d93a1/build.sh | 10 +++++----- recipes/samtools/1.9+37-g5708485/build.sh | 10 +++++----- recipes/teepot/1.2.0/build.sh | 7 +++++-- recipes/tophat2/2.1.1/build.sh | 4 +--- recipes/xz/5.2.3/build.sh | 5 +++-- recipes/zlib/1.2.11/build.sh | 7 ++++++- 16 files changed, 60 insertions(+), 53 deletions(-) diff --git a/recipes/baton/1.1.0/build.sh b/recipes/baton/1.1.0/build.sh index b2dd5785..535cae3e 100755 --- a/recipes/baton/1.1.0/build.sh +++ b/recipes/baton/1.1.0/build.sh @@ -6,11 +6,10 @@ n="$CPU_COUNT" export LD_LIBRARY_PATH="$PREFIX/lib" -CPPFLAGS="-I$PREFIX/include -I$PREFIX/include/irods" \ - LDFLAGS="-L$PREFIX/lib -L$PREFIX/lib/irods/externals" \ - ./configure --prefix="$PREFIX" --with-irods="$PREFIX" +./configure --prefix="$PREFIX" \ + --with-irods="$PREFIX" \ + CPPFLAGS="-I$PREFIX/include -I$PREFIX/include/irods" \ + LDFLAGS="-L$PREFIX/lib -L$PREFIX/lib/irods/externals" -make -j $n \ - CPPFLAGS="-I$PREFIX/include -I$PREFIX/include/irods" \ - LDFLAGS="-L$PREFIX/lib -L$PREFIX/lib/irods/externals" +make -j $n make install prefix="$PREFIX" diff --git a/recipes/bowtie2/2.2.7/build.sh b/recipes/bowtie2/2.2.7/build.sh index 2ad5ef89..bf9125e6 100755 --- a/recipes/bowtie2/2.2.7/build.sh +++ b/recipes/bowtie2/2.2.7/build.sh @@ -4,7 +4,8 @@ set -ex n="$CPU_COUNT" -make -j $n prefix="$PREFIX" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make -j "$n" prefix="$PREFIX" \ + CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" # There is no install target in the Makefile mkdir -p "$PREFIX/bin" diff --git a/recipes/fastx_toolkit/0.0.14/build.sh b/recipes/fastx_toolkit/0.0.14/build.sh index 3ba14a7c..63b3ba41 100755 --- a/recipes/fastx_toolkit/0.0.14/build.sh +++ b/recipes/fastx_toolkit/0.0.14/build.sh @@ -6,12 +6,12 @@ n="$CPU_COUNT" pushd gtextutils ./configure --prefix="$PREFIX" -make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make -j "$n" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install prefix="$PREFIX" popd pushd fastx_toolkit ./configure --prefix="$PREFIX" -make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make -j "$n" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install prefix="$PREFIX" popd diff --git a/recipes/htslib/1.9+47-gc93b673/build.sh b/recipes/htslib/1.9+47-gc93b673/build.sh index 612cdad2..95871e80 100755 --- a/recipes/htslib/1.9+47-gc93b673/build.sh +++ b/recipes/htslib/1.9+47-gc93b673/build.sh @@ -10,13 +10,13 @@ cp aclocal.m4 aclocal.m4.tmp autoreconf cp aclocal.m4.tmp aclocal.m4 -CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" \ - ./configure --prefix="$PREFIX" \ - --enable-libcurl \ - --enable-plugins +./configure \ + --prefix="$PREFIX" \ + --enable-libcurl \ + --enable-plugins \ + CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make -j $n AR="$AR" CC="$GCC" \ - CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make -j $n AR="$AR" make install prefix="$PREFIX" popd diff --git a/recipes/htslib/1.9+66_gbcf9bff/build.sh b/recipes/htslib/1.9+66_gbcf9bff/build.sh index 612cdad2..95871e80 100755 --- a/recipes/htslib/1.9+66_gbcf9bff/build.sh +++ b/recipes/htslib/1.9+66_gbcf9bff/build.sh @@ -10,13 +10,13 @@ cp aclocal.m4 aclocal.m4.tmp autoreconf cp aclocal.m4.tmp aclocal.m4 -CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" \ - ./configure --prefix="$PREFIX" \ - --enable-libcurl \ - --enable-plugins +./configure \ + --prefix="$PREFIX" \ + --enable-libcurl \ + --enable-plugins \ + CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make -j $n AR="$AR" CC="$GCC" \ - CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make -j $n AR="$AR" make install prefix="$PREFIX" popd diff --git a/recipes/htslib/1.9+9-g6ec3b94/build.sh b/recipes/htslib/1.9+9-g6ec3b94/build.sh index f3962294..95871e80 100755 --- a/recipes/htslib/1.9+9-g6ec3b94/build.sh +++ b/recipes/htslib/1.9+9-g6ec3b94/build.sh @@ -10,13 +10,13 @@ cp aclocal.m4 aclocal.m4.tmp autoreconf cp aclocal.m4.tmp aclocal.m4 -CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" ./configure \ - --prefix="$PREFIX" \ - --enable-libcurl \ - --enable-plugins - -make -j $n AR="$AR" CC="$GCC" \ - CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +./configure \ + --prefix="$PREFIX" \ + --enable-libcurl \ + --enable-plugins \ + CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" + +make -j $n AR="$AR" make install prefix="$PREFIX" popd diff --git a/recipes/jansson/2.1.0/build.sh b/recipes/jansson/2.1.0/build.sh index 2b038685..e8aeec2e 100755 --- a/recipes/jansson/2.1.0/build.sh +++ b/recipes/jansson/2.1.0/build.sh @@ -7,9 +7,8 @@ n="$CPU_COUNT" autoreconf -fi ./configure --prefix="$PREFIX" \ CPPFLAGS="-I$PREFIX/include" \ - LDFLAGS="-L$PREFIX/lib" + LDFLAGS="-Wl,--disable-new-dtags -L$PREFIX/lib" -make -j $n CPPFLAGS="-I$PREFIX/include" \ - LDFLAGS="-Wl,--disable-new-dtags -L$PREFIX/lib" +make -j "$n" make install prefix="$PREFIX" diff --git a/recipes/jq/1.5/build.sh b/recipes/jq/1.5/build.sh index 52f67cc4..a144d852 100755 --- a/recipes/jq/1.5/build.sh +++ b/recipes/jq/1.5/build.sh @@ -6,5 +6,5 @@ n="$CPU_COUNT" ./configure --prefix="$PREFIX" --disable-maintainer-mode -make -j $n LDFLAGS=-all-static +make -j "$n" LDFLAGS=-all-static make install prefix="$PREFIX" diff --git a/recipes/libgd/2.2.5/build.sh b/recipes/libgd/2.2.5/build.sh index b93b9b98..4b67e9c4 100644 --- a/recipes/libgd/2.2.5/build.sh +++ b/recipes/libgd/2.2.5/build.sh @@ -13,7 +13,8 @@ n="$CPU_COUNT" --without-tiff \ --without-webp \ --without-xpm \ - --with-zlib + --with-zlib \ + CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX" -make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX" +make -j "$n" make install prefix="$PREFIX" diff --git a/recipes/libpng/1.6.34/build.sh b/recipes/libpng/1.6.34/build.sh index f669fa27..f4a362fd 100644 --- a/recipes/libpng/1.6.34/build.sh +++ b/recipes/libpng/1.6.34/build.sh @@ -8,5 +8,5 @@ n="$CPU_COUNT" CPPFLAGS="-I$PREFIX/include" \ LDFLAGS="-L$PREFIX/lib" -make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make -j "$n" make install prefix="$PREFIX" diff --git a/recipes/samtools/1.9+2-g02d93a1/build.sh b/recipes/samtools/1.9+2-g02d93a1/build.sh index c5daf803..f71d11c6 100755 --- a/recipes/samtools/1.9+2-g02d93a1/build.sh +++ b/recipes/samtools/1.9+2-g02d93a1/build.sh @@ -6,12 +6,12 @@ n="$CPU_COUNT" autoreconf -CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" \ - ./configure --prefix="$PREFIX" \ - --with-htslib=system \ - --without-curses +./configure --prefix="$PREFIX" \ + --with-htslib=system \ + --without-curses \ + CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make -j $n AR="$AR" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make -j $n AR="$AR" make install prefix="$PREFIX" mkdir p "$PREFIX/include/samtools" diff --git a/recipes/samtools/1.9+37-g5708485/build.sh b/recipes/samtools/1.9+37-g5708485/build.sh index c5daf803..f71d11c6 100755 --- a/recipes/samtools/1.9+37-g5708485/build.sh +++ b/recipes/samtools/1.9+37-g5708485/build.sh @@ -6,12 +6,12 @@ n="$CPU_COUNT" autoreconf -CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" \ - ./configure --prefix="$PREFIX" \ - --with-htslib=system \ - --without-curses +./configure --prefix="$PREFIX" \ + --with-htslib=system \ + --without-curses \ + CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make -j $n AR="$AR" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make -j $n AR="$AR" make install prefix="$PREFIX" mkdir p "$PREFIX/include/samtools" diff --git a/recipes/teepot/1.2.0/build.sh b/recipes/teepot/1.2.0/build.sh index 294d1e39..a56825fd 100755 --- a/recipes/teepot/1.2.0/build.sh +++ b/recipes/teepot/1.2.0/build.sh @@ -2,7 +2,10 @@ set -ex -./configure --prefix="$PREFIX" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +n="$CPU_COUNT" -make CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib -lpthread" +./configure --prefix="$PREFIX" \ + CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib -lpthread" + +make -j "$n" make install prefix="$PREFIX" diff --git a/recipes/tophat2/2.1.1/build.sh b/recipes/tophat2/2.1.1/build.sh index 7dde45a9..bfbf6934 100755 --- a/recipes/tophat2/2.1.1/build.sh +++ b/recipes/tophat2/2.1.1/build.sh @@ -9,7 +9,5 @@ n=1 --with-boost="$PREFIX" \ CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make -j $n CC="$GCC" \ - INCLUDES="-I. -I$PREFIX/include" LIBPATH="-L$PREFIX/lib" \ - CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make -j "$n" CC="$GCC" INCLUDES="-I. -I$PREFIX/include" LIBPATH="-L$PREFIX/lib" make install prefix="$PREFIX" diff --git a/recipes/xz/5.2.3/build.sh b/recipes/xz/5.2.3/build.sh index 68c44cfd..895b195c 100644 --- a/recipes/xz/5.2.3/build.sh +++ b/recipes/xz/5.2.3/build.sh @@ -4,6 +4,7 @@ set -ex n="$CPU_COUNT" -./configure prefix="$PREFIX" -make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +./configure prefix="$PREFIX" \ + CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make -j "$n" make install diff --git a/recipes/zlib/1.2.11/build.sh b/recipes/zlib/1.2.11/build.sh index e3885af6..5791dd82 100644 --- a/recipes/zlib/1.2.11/build.sh +++ b/recipes/zlib/1.2.11/build.sh @@ -4,6 +4,11 @@ set -ex n="$CPU_COUNT" +# This is not a configure script that was generated by GNU +# autoconf. It does not process extra comman line options, which is +# why configuration is set in the environment and passed as arguments +# to make. prefix="$PREFIX" CC="$GCC" ./configure -make -j $n CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" + +make -j "$n" CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" make install From 7c4ae46c52c35819c29edb1cdd94583cd1eb5713 Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 7 May 2019 14:20:59 +0100 Subject: [PATCH 083/119] Added samtools interim build 1.9+48_g2d4907 --- recipes/samtools/1.9+48-g2d4907c/README.md | 2 + recipes/samtools/1.9+48-g2d4907c/build.sh | 19 ++++++ recipes/samtools/1.9+48-g2d4907c/meta.yaml | 75 ++++++++++++++++++++++ 3 files changed, 96 insertions(+) create mode 100644 recipes/samtools/1.9+48-g2d4907c/README.md create mode 100755 recipes/samtools/1.9+48-g2d4907c/build.sh create mode 100644 recipes/samtools/1.9+48-g2d4907c/meta.yaml diff --git a/recipes/samtools/1.9+48-g2d4907c/README.md b/recipes/samtools/1.9+48-g2d4907c/README.md new file mode 100644 index 00000000..c4d939bd --- /dev/null +++ b/recipes/samtools/1.9+48-g2d4907c/README.md @@ -0,0 +1,2 @@ +This post release build was created from the develop branch of +samtools to include the most recent stats fixes. \ No newline at end of file diff --git a/recipes/samtools/1.9+48-g2d4907c/build.sh b/recipes/samtools/1.9+48-g2d4907c/build.sh new file mode 100755 index 00000000..dfa64c6d --- /dev/null +++ b/recipes/samtools/1.9+48-g2d4907c/build.sh @@ -0,0 +1,19 @@ +#!/bin/sh + +set -ex + +n="$CPU_COUNT" + +autoreconf + +./configure --prefix="$PREFIX" \ + --with-htslib=system \ + --without-curses \ + CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" + +make -j "$n" AR="$AR" +make install prefix="$PREFIX" + +mkdir p "$PREFIX/include/samtools" +cp "$SRC_DIR/"*.h "$PREFIX/include/samtools/" +cp "$SRC_DIR/libbam.a" "$PREFIX/lib" diff --git a/recipes/samtools/1.9+48-g2d4907c/meta.yaml b/recipes/samtools/1.9+48-g2d4907c/meta.yaml new file mode 100644 index 00000000..33f38ff5 --- /dev/null +++ b/recipes/samtools/1.9+48-g2d4907c/meta.yaml @@ -0,0 +1,75 @@ +{% set version = "1.9+48_g2d4907c" %} +{% set htslib_version = "1.9+66_gbcf9bff" %} + +package: + name: samtools + version: "{{ version }}" + +about: + home: https://github.com/samtools/samtools + license: MIT + summary: C library for high-throughput sequencing data formats. + +build: + number: 1 + +source: + git_url: https://github.com/samtools/samtools.git + git_rev: 2d4907cf9a34ccf7cde60143158b39e1cb40ac0c + +requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - libhts-dev =={{ htslib_version }} + - libz-dev + run: + - libhts =={{ htslib_version }} + - libz + +outputs: + - name: samtools-bin + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - libhts-dev =={{ htslib_version }} + - libz-dev + run: + - libhts =={{ htslib_version }} + - libz + files: + - bin/ace2sam + - bin/maq2sam-* + - bin/md5* + - bin/plot-bamstats + - bin/samtools + - bin/wgsim + - bin/*.pl + - bin/*.py + test: + commands: + - echo '@HD VN:1.0 SO:coordinate' | samtools view + + - name: samtools-dev + version: {{ version }} + requirements: + run: + - libhts =={{ htslib_version }} + - libz + files: + - include/samtools/*.h + - lib/libbam.a + test: + commands: + - test -f ${PREFIX}/include/samtools/sam.h + - test -f ${PREFIX}/lib/libbam.a From 717f4c0c8c5213245744f66233a0d7797922d2c0 Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 7 May 2019 14:29:40 +0100 Subject: [PATCH 084/119] Pin to a specific htslib interim build to avoid potential compatibility errors before the next htslib release. --- recipes/npg_qc_utils/65.0/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/npg_qc_utils/65.0/meta.yaml b/recipes/npg_qc_utils/65.0/meta.yaml index 12dc5527..bb5135b6 100644 --- a/recipes/npg_qc_utils/65.0/meta.yaml +++ b/recipes/npg_qc_utils/65.0/meta.yaml @@ -1,4 +1,5 @@ {% set version = "65.0" %} +{% set htslib_version = "1.9+66_gbcf9bff" %} package: name: npg_qc_utils @@ -21,11 +22,11 @@ requirements: - {{ compiler("c") }} - make host: - - libhts-dev + - libhts-dev =={{ htslib_version }} - samtools-dev - libz-dev run: - - libhts + - libhts =={{ htslib_version }} - libz test: From 5844ce65536a7558d56af5852180f0ea32c2b25d Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 7 May 2019 16:38:51 +0100 Subject: [PATCH 085/119] Added specialised bwa 0.5.10-mt_fixes.2 --- recipes/bwa/0.5.10-mt_fixes.2/Makefile.patch | 19 ++++++++++++ recipes/bwa/0.5.10-mt_fixes.2/build.sh | 16 ++++++++++ recipes/bwa/0.5.10-mt_fixes.2/meta.yaml | 32 ++++++++++++++++++++ 3 files changed, 67 insertions(+) create mode 100644 recipes/bwa/0.5.10-mt_fixes.2/Makefile.patch create mode 100644 recipes/bwa/0.5.10-mt_fixes.2/build.sh create mode 100644 recipes/bwa/0.5.10-mt_fixes.2/meta.yaml diff --git a/recipes/bwa/0.5.10-mt_fixes.2/Makefile.patch b/recipes/bwa/0.5.10-mt_fixes.2/Makefile.patch new file mode 100644 index 00000000..76b607f8 --- /dev/null +++ b/recipes/bwa/0.5.10-mt_fixes.2/Makefile.patch @@ -0,0 +1,19 @@ +*** Makefile 2018-09-19 11:30:16.323723930 +0000 +--- Makefile.1 2018-09-19 11:29:44.126713296 +0000 +*************** +*** 41,47 **** + + bwa:bwt_gen/libbwtgen.a $(OBJS) main.c main.h + d=`date`;\ +! $(CC) $(CFLAGS) -DBLDDATE="$$d" -c main.c -o main.o ;\ + $(CC) $(CFLAGS) $(DFLAGS) $(OBJS) main.o -o $@ $(LIBS) + + depend: +--- 41,47 ---- + + bwa:bwt_gen/libbwtgen.a $(OBJS) main.c main.h + d=`date`;\ +! $(CC) $(CFLAGS) -DBLDDATE="$$d" $(INCLUDES) -c main.c -o main.o ;\ + $(CC) $(CFLAGS) $(DFLAGS) $(OBJS) main.o -o $@ $(LIBS) + + depend: diff --git a/recipes/bwa/0.5.10-mt_fixes.2/build.sh b/recipes/bwa/0.5.10-mt_fixes.2/build.sh new file mode 100644 index 00000000..07ffc4a7 --- /dev/null +++ b/recipes/bwa/0.5.10-mt_fixes.2/build.sh @@ -0,0 +1,16 @@ +#!/bin/sh + +set -ex + +n="$CPU_COUNT" + +make -j "$n" AR="$AR" CC="$GCC" \ + CFLAGS="-g -Wall -O2 --std=gnu89" \ + INCLUDES="-I. -I.. -I$PREFIX/include" \ + LIBS="-L$PREFIX/lib -lm -lz -lpthread -Lbwt_gen -lbwtgen" + +mkdir -p "$PREFIX/bin" +cp bwa "$PREFIX/bin/" + +mkdir -p "$PREFIX/share/man/man1" +cp bwa.1 "$PREFIX/share/man/man1/" diff --git a/recipes/bwa/0.5.10-mt_fixes.2/meta.yaml b/recipes/bwa/0.5.10-mt_fixes.2/meta.yaml new file mode 100644 index 00000000..b136ba96 --- /dev/null +++ b/recipes/bwa/0.5.10-mt_fixes.2/meta.yaml @@ -0,0 +1,32 @@ +{% set version = "0.5.10_mt_fixes.2" %} + +package: + name: bwa + version: "{{ version }}" + +about: + home: https://github.com/lh3/bwa + license: GPL3 + summary: Burrows-Wheeler Aligner for short-read alignment. + +build: + number: 1 + +source: + git_url: https://github.com/wtsi-npg/bwa.git + git_rev: b8267d812d44036f5858baf3353fa5f4ceca06f8 + patches: + - Makefile.patch + +requirements: + build: + - {{ compiler("c") }} + - make + host: + - libz-dev + run: + - libz + +test: + commands: + - test -x ${PREFIX}/bin/bwa From 0c489f448b5b5aa6e66ec93ac8e1a8cf873c1f00 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Wed, 8 May 2019 13:38:34 +0100 Subject: [PATCH 086/119] npg_qc_utils v 67.0 build --- recipes/npg_qc_utils/67.0/build.sh | 27 ++++++++++++++++++++++++ recipes/npg_qc_utils/67.0/meta.yaml | 32 +++++++++++++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100755 recipes/npg_qc_utils/67.0/build.sh create mode 100644 recipes/npg_qc_utils/67.0/meta.yaml diff --git a/recipes/npg_qc_utils/67.0/build.sh b/recipes/npg_qc_utils/67.0/build.sh new file mode 100755 index 00000000..745f25db --- /dev/null +++ b/recipes/npg_qc_utils/67.0/build.sh @@ -0,0 +1,27 @@ +#!/bin/sh + +set -e + +n=`expr $CPU_COUNT / 4 \| 1` + +pushd samtools +./configure --prefix="$PREFIX" --without-curses +make -j $n CFLAGS="-fPIC" +ln -s . include +popd + +pushd npg_qc_utils + +pushd norm_fit +mkdir -p build +make -j $n INCLUDES="-I. -I$PREFIX/include" LIBPATH="-L$PREFIX/lib" +cp ./build/norm_fit "$PREFIX/bin/" +popd + +pushd gt_utils +mkdir -p build +make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make install installdir="$PREFIX/bin" +popd + +popd diff --git a/recipes/npg_qc_utils/67.0/meta.yaml b/recipes/npg_qc_utils/67.0/meta.yaml new file mode 100644 index 00000000..059fcc46 --- /dev/null +++ b/recipes/npg_qc_utils/67.0/meta.yaml @@ -0,0 +1,32 @@ +{% set version = "67.0" %} + +package: + name: npg_qc_utils + version: "{{ version }}" + +about: + home: https://github.com/wtsi-npg/npg_qc_utils + license: GPLv3 + summary: "C programs extracted from npg_qc." + +build: + number: 0 + +source: + - git_url: https://github.com/wtsi-npg/npg_qc_utils.git + git_rev: {{ version }} + folder: npg_qc_utils + +requirements: + build: + - gcc_npg >=7.3 + - zlib + + run: + - zlib + +test: + commands: + - ${PREFIX}/bin/find_gt_match -h + - ${PREFIX}/bin/gt_pack -h + - test -e ${PREFIX}/bin/norm_fit From f91128df76e73e91deea7e1f120ef217efe410c6 Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Thu, 9 May 2019 11:49:09 +0000 Subject: [PATCH 087/119] add wr 0.18.0 --- recipes/wr/0.18.0/build.sh | 12 ++++++++++++ recipes/wr/0.18.0/meta.yaml | 24 ++++++++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 recipes/wr/0.18.0/build.sh create mode 100644 recipes/wr/0.18.0/meta.yaml diff --git a/recipes/wr/0.18.0/build.sh b/recipes/wr/0.18.0/build.sh new file mode 100644 index 00000000..f093a2c3 --- /dev/null +++ b/recipes/wr/0.18.0/build.sh @@ -0,0 +1,12 @@ +#!/bin/sh + +set -e + +mkdir -p "$PREFIX/bin" +cp wr "$PREFIX/bin/" + +mkdir -p "$PREFIX/etc" +cp wr_config.yml "$PREFIX/etc/" + +mkdir -p "$PREFIX/share/doc/wr" +cp README.md "$PREFIX/share/doc/wr/" diff --git a/recipes/wr/0.18.0/meta.yaml b/recipes/wr/0.18.0/meta.yaml new file mode 100644 index 00000000..b9349713 --- /dev/null +++ b/recipes/wr/0.18.0/meta.yaml @@ -0,0 +1,24 @@ +{% set version = "0.18.0" %} +{% set sha256 = "4e02580364635cefdc6c0f3d1a8b63ed3b5d6b103677cd907e5491c683614de2" %} + +package: + name: wr + version: "{{ version }}" + +about: + home: https://github.com/VertebrateResequencing/wr + license: GPLv3 + summary: "High performance Workflow Runner." + +build: + number: 0 + binary_relocation: false + +source: + url: https://github.com/VertebrateResequencing/wr/releases/download/v{{ version }}/wr-linux-x86-64.zip + fn: wr-{{ version }}.zip + sha256: {{ sha256 }} + +test: + commands: + - wr -h From c88f2a7dddcb48520684a7dc034a4f8a7d034327 Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Tue, 21 May 2019 09:54:11 +0100 Subject: [PATCH 088/119] add recipe for npg_qc_utils 67.0 --- recipes/npg_qc_utils/67.0/build.sh | 20 ++++++++++++++++++ recipes/npg_qc_utils/67.0/meta.yaml | 32 +++++++++++++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 recipes/npg_qc_utils/67.0/build.sh create mode 100644 recipes/npg_qc_utils/67.0/meta.yaml diff --git a/recipes/npg_qc_utils/67.0/build.sh b/recipes/npg_qc_utils/67.0/build.sh new file mode 100644 index 00000000..5daf2de8 --- /dev/null +++ b/recipes/npg_qc_utils/67.0/build.sh @@ -0,0 +1,20 @@ +#!/bin/sh + +set -ex + +n="$CPU_COUNT" + +pushd norm_fit +mkdir -p build +make -j $n CC="$GCC" \ + LIBPATH="-L$PREFIX/lib" +cp ./build/norm_fit "$PREFIX/bin/" +popd + +pushd gt_utils +mkdir -p build +make -j $n CC="$GCC" \ + CPPFLAGS="-I$PREFIX/include" \ + LDFLAGS="-L$PREFIX/lib" +make install installdir="$PREFIX/bin" +popd diff --git a/recipes/npg_qc_utils/67.0/meta.yaml b/recipes/npg_qc_utils/67.0/meta.yaml new file mode 100644 index 00000000..95488159 --- /dev/null +++ b/recipes/npg_qc_utils/67.0/meta.yaml @@ -0,0 +1,32 @@ +{% set version = "67.0" %} + +package: + name: npg_qc_utils + version: "{{ version }}" + +about: + home: https://github.com/wtsi-npg/npg_qc_utils + license: GPLv3 + summary: "C programs extracted from npg_qc." + +build: + number: 0 + +source: + - git_url: https://github.com/wtsi-npg/npg_qc_utils.git + git_rev: {{ version }} + +requirements: + build: + - {{ compiler("c") }} + - make + host: + - libz-dev + run: + - libz + +test: + commands: + - ${PREFIX}/bin/find_gt_match -h + - ${PREFIX}/bin/gt_pack -h + - test -e ${PREFIX}/bin/norm_fit From 944c023b879f659bba48779b626fcd62db22c6d8 Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Thu, 9 May 2019 13:15:08 +0000 Subject: [PATCH 089/119] add io_lib 1.14.9 --- recipes/io_lib/1.14.9/build.sh | 11 +++ recipes/io_lib/1.14.9/meta.yaml | 154 ++++++++++++++++++++++++++++++++ 2 files changed, 165 insertions(+) create mode 100755 recipes/io_lib/1.14.9/build.sh create mode 100644 recipes/io_lib/1.14.9/meta.yaml diff --git a/recipes/io_lib/1.14.9/build.sh b/recipes/io_lib/1.14.9/build.sh new file mode 100755 index 00000000..f5f91d65 --- /dev/null +++ b/recipes/io_lib/1.14.9/build.sh @@ -0,0 +1,11 @@ +#!/bin/sh + +set -ex + +n="$CPU_COUNT" + +./configure --prefix="$PREFIX" --with-zlib="$PREFIX" --with-libcurl="$PREFIX" + +make -j $n CPPFLAGS="-I$PREFIX/include" \ + LDFLAGS="-Wl,-rpath-link,$PREFIX/lib -Wl,--disable-new-dtags -L$PREFIX/lib" +make install prefix="$PREFIX" diff --git a/recipes/io_lib/1.14.9/meta.yaml b/recipes/io_lib/1.14.9/meta.yaml new file mode 100644 index 00000000..7c686c99 --- /dev/null +++ b/recipes/io_lib/1.14.9/meta.yaml @@ -0,0 +1,154 @@ +{% set version = "1.14.9" %} +{% set sha256 = "8d0732f3d37abba1633731bfacac5fd7f8172eccb1cef224e8ced904d3b242f4" %} + +package: + name: io_lib + version: "{{ version }}" + +about: + home: https://sourceforge.net/projects/staden + license: BSD + summary: DNA sequence assembly, editing and analysis tools. + +build: + number: 0 + +source: + url: https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-14-9/io_lib-{{ version }}.tar.gz + fn: io_lib-{{ version }}.tar.gz + sha256: {{ sha256 }} + +requirements: + build: + - {{ compiler("c") }} + - autoconf + - make + host: + - irods-dev >=4.1.12 + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libz-dev + run: + - libbz2 + - libcurl + - liblzma + - libz + +outputs: + - name: io_lib-bin + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + host: + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libz-dev + run: + - {{ pin_subpackage("libstaden-read", exact=True) }} + - libbz2 + - libcurl + - liblzma + - libz + files: + - bin/append_sff + - bin/convert_trace + - bin/cram_dump + - bin/cram_filter + - bin/cram_index + - bin/cram_size + - bin/extract_fastq + - bin/extract_qual + - bin/extract_seq + - bin/get_comment + - bin/hash_exp + - bin/hash_extract + - bin/hash_list + - bin/hash_sff + - bin/hash_tar + - bin/index_tar + - bin/makeSCF + - bin/scf_dump + - bin/scf_info + - bin/scf_update + - bin/scram_flagstat + - bin/scram_merge + - bin/scram_pileup + - bin/scram_test + - bin/scramble + - bin/srf2fasta + - bin/srf2fastq + - bin/srf_dump_all + - bin/srf_extract_hash + - bin/srf_extract_linear + - bin/srf_filter + - bin/srf_index_hash + - bin/srf_info + - bin/srf_list + - bin/trace_dump + - bin/ztr_dump + - share/man/man1/scramble.1 + - share/man/man1/srf2fasta.1 + - share/man/man1/srf2fastq.1 + - share/man/man1/srf_index_hash.1 + - share/man/man1/srf_info.1 + - share/man/man1/srf_list.1 + test: + commands: + - scramble -h + + - name: libstaden-read + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + host: + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libz-dev + run: + - libbz2 + - libcurl + - liblzma + - libz + files: + - lib/libstaden-read* + test: + commands: + - test -f ${PREFIX}/lib/libstaden-read.a + - test -h ${PREFIX}/lib/libstaden-read.so + + - name: libstaden-read-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libstaden-read", exact=True) }} + files: + - bin/io_lib-config + - include/io_lib + - share/man/man3/ExperimentFile.3 + - share/man/man3/exp2read.3 + - share/man/man3/fread_reading.3 + - share/man/man3/fread_scf.3 + - share/man/man3/fwrite_reading.3 + - share/man/man3/fwrite_scf.3 + - share/man/man3/read2exp.3 + - share/man/man3/read2scf.3 + - share/man/man3/read_allocate.3 + - share/man/man3/read_deallocate.3 + - share/man/man3/read_reading.3 + - share/man/man3/read_scf.3 + - share/man/man3/read_scf_header.3 + - share/man/man3/scf2read.3 + - share/man/man3/write_reading.3 + - share/man/man3/write_scf.3 + - share/man/man3/write_scf_header.3 + - share/man/man4/Read.4 + test: + commands: + - test -f ${PREFIX}/include/io_lib/io_lib_config.h From a5c59fa2a40c4d219348d56e2ef9c3f8e7829010 Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Wed, 22 May 2019 16:23:11 +0100 Subject: [PATCH 090/119] pass all build flags to configure not to make affects io_lib 1.14.9 & 1.14.11 new build for 1.14.11 --- recipes/io_lib/1.14.11/build.sh | 14 +++++++++----- recipes/io_lib/1.14.11/meta.yaml | 2 +- recipes/io_lib/1.14.9/build.sh | 14 +++++++++----- 3 files changed, 19 insertions(+), 11 deletions(-) diff --git a/recipes/io_lib/1.14.11/build.sh b/recipes/io_lib/1.14.11/build.sh index f5f91d65..8a5e46cd 100755 --- a/recipes/io_lib/1.14.11/build.sh +++ b/recipes/io_lib/1.14.11/build.sh @@ -4,8 +4,12 @@ set -ex n="$CPU_COUNT" -./configure --prefix="$PREFIX" --with-zlib="$PREFIX" --with-libcurl="$PREFIX" - -make -j $n CPPFLAGS="-I$PREFIX/include" \ - LDFLAGS="-Wl,-rpath-link,$PREFIX/lib -Wl,--disable-new-dtags -L$PREFIX/lib" -make install prefix="$PREFIX" +./configure \ + --prefix="$PREFIX" \ + --with-zlib="$PREFIX" \ + --with-libcurl="$PREFIX" \ + CPPFLAGS="-I$PREFIX/include" \ + LDFLAGS="-Wl,-rpath-link,$PREFIX/lib -Wl,--disable-new-dtags -L$PREFIX/lib" + +make -j "$n" +make install diff --git a/recipes/io_lib/1.14.11/meta.yaml b/recipes/io_lib/1.14.11/meta.yaml index b63e9bf6..eb902558 100644 --- a/recipes/io_lib/1.14.11/meta.yaml +++ b/recipes/io_lib/1.14.11/meta.yaml @@ -11,7 +11,7 @@ about: summary: DNA sequence assembly, editing and analysis tools. build: - number: 0 + number: 1 source: url: https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-14-11/io_lib-{{ version }}.tar.gz diff --git a/recipes/io_lib/1.14.9/build.sh b/recipes/io_lib/1.14.9/build.sh index f5f91d65..8a5e46cd 100755 --- a/recipes/io_lib/1.14.9/build.sh +++ b/recipes/io_lib/1.14.9/build.sh @@ -4,8 +4,12 @@ set -ex n="$CPU_COUNT" -./configure --prefix="$PREFIX" --with-zlib="$PREFIX" --with-libcurl="$PREFIX" - -make -j $n CPPFLAGS="-I$PREFIX/include" \ - LDFLAGS="-Wl,-rpath-link,$PREFIX/lib -Wl,--disable-new-dtags -L$PREFIX/lib" -make install prefix="$PREFIX" +./configure \ + --prefix="$PREFIX" \ + --with-zlib="$PREFIX" \ + --with-libcurl="$PREFIX" \ + CPPFLAGS="-I$PREFIX/include" \ + LDFLAGS="-Wl,-rpath-link,$PREFIX/lib -Wl,--disable-new-dtags -L$PREFIX/lib" + +make -j "$n" +make install From 115a5c661ee18486f2d8a6058551c29e62c52cb6 Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Thu, 23 May 2019 08:47:21 +0000 Subject: [PATCH 091/119] add wr 0.18.1 --- recipes/wr/0.18.1/build.sh | 12 ++++++++++++ recipes/wr/0.18.1/meta.yaml | 24 ++++++++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 recipes/wr/0.18.1/build.sh create mode 100644 recipes/wr/0.18.1/meta.yaml diff --git a/recipes/wr/0.18.1/build.sh b/recipes/wr/0.18.1/build.sh new file mode 100644 index 00000000..f093a2c3 --- /dev/null +++ b/recipes/wr/0.18.1/build.sh @@ -0,0 +1,12 @@ +#!/bin/sh + +set -e + +mkdir -p "$PREFIX/bin" +cp wr "$PREFIX/bin/" + +mkdir -p "$PREFIX/etc" +cp wr_config.yml "$PREFIX/etc/" + +mkdir -p "$PREFIX/share/doc/wr" +cp README.md "$PREFIX/share/doc/wr/" diff --git a/recipes/wr/0.18.1/meta.yaml b/recipes/wr/0.18.1/meta.yaml new file mode 100644 index 00000000..8a730da9 --- /dev/null +++ b/recipes/wr/0.18.1/meta.yaml @@ -0,0 +1,24 @@ +{% set version = "0.18.1" %} +{% set sha256 = "fc6fe106a6a03f27ea994f1afcacdb803259bbb80707756cd8c70877b725df01" %} + +package: + name: wr + version: "{{ version }}" + +about: + home: https://github.com/VertebrateResequencing/wr + license: GPLv3 + summary: "High performance Workflow Runner." + +build: + number: 0 + binary_relocation: false + +source: + url: https://github.com/VertebrateResequencing/wr/releases/download/v{{ version }}/wr-linux-x86-64.zip + fn: wr-{{ version }}.zip + sha256: {{ sha256 }} + +test: + commands: + - wr -h From 4fb669d69c51700b51f56ff8c69454182d60bb28 Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Thu, 23 May 2019 09:51:21 +0100 Subject: [PATCH 092/119] add wr 0.18.1 --- recipes/wr/0.18.1/build.sh | 12 ++++++++++++ recipes/wr/0.18.1/meta.yaml | 24 ++++++++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 recipes/wr/0.18.1/build.sh create mode 100644 recipes/wr/0.18.1/meta.yaml diff --git a/recipes/wr/0.18.1/build.sh b/recipes/wr/0.18.1/build.sh new file mode 100644 index 00000000..f093a2c3 --- /dev/null +++ b/recipes/wr/0.18.1/build.sh @@ -0,0 +1,12 @@ +#!/bin/sh + +set -e + +mkdir -p "$PREFIX/bin" +cp wr "$PREFIX/bin/" + +mkdir -p "$PREFIX/etc" +cp wr_config.yml "$PREFIX/etc/" + +mkdir -p "$PREFIX/share/doc/wr" +cp README.md "$PREFIX/share/doc/wr/" diff --git a/recipes/wr/0.18.1/meta.yaml b/recipes/wr/0.18.1/meta.yaml new file mode 100644 index 00000000..8a730da9 --- /dev/null +++ b/recipes/wr/0.18.1/meta.yaml @@ -0,0 +1,24 @@ +{% set version = "0.18.1" %} +{% set sha256 = "fc6fe106a6a03f27ea994f1afcacdb803259bbb80707756cd8c70877b725df01" %} + +package: + name: wr + version: "{{ version }}" + +about: + home: https://github.com/VertebrateResequencing/wr + license: GPLv3 + summary: "High performance Workflow Runner." + +build: + number: 0 + binary_relocation: false + +source: + url: https://github.com/VertebrateResequencing/wr/releases/download/v{{ version }}/wr-linux-x86-64.zip + fn: wr-{{ version }}.zip + sha256: {{ sha256 }} + +test: + commands: + - wr -h From 50b27e27f4998db208ea39b47524f11b35337ae7 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Thu, 23 May 2019 11:31:36 +0100 Subject: [PATCH 093/119] fully remove dependency on samtools --- recipes/npg_qc_utils/67.0/build.sh | 6 ------ 1 file changed, 6 deletions(-) diff --git a/recipes/npg_qc_utils/67.0/build.sh b/recipes/npg_qc_utils/67.0/build.sh index 745f25db..db565223 100755 --- a/recipes/npg_qc_utils/67.0/build.sh +++ b/recipes/npg_qc_utils/67.0/build.sh @@ -4,12 +4,6 @@ set -e n=`expr $CPU_COUNT / 4 \| 1` -pushd samtools -./configure --prefix="$PREFIX" --without-curses -make -j $n CFLAGS="-fPIC" -ln -s . include -popd - pushd npg_qc_utils pushd norm_fit From 3a7269623027f47cfa567de54bbab19a02cd0504 Mon Sep 17 00:00:00 2001 From: "David K. Jackson" Date: Wed, 29 May 2019 09:58:20 +0000 Subject: [PATCH 094/119] remove use of configure --with-libcurl= and --with-zlib= which conflict with configure LDFLAGS= argument --- recipes/io_lib/1.14.11/build.sh | 2 -- recipes/io_lib/1.14.11/meta.yaml | 2 +- recipes/io_lib/1.14.9/build.sh | 2 -- recipes/io_lib/1.14.9/meta.yaml | 2 +- 4 files changed, 2 insertions(+), 6 deletions(-) diff --git a/recipes/io_lib/1.14.11/build.sh b/recipes/io_lib/1.14.11/build.sh index 8a5e46cd..8a151372 100755 --- a/recipes/io_lib/1.14.11/build.sh +++ b/recipes/io_lib/1.14.11/build.sh @@ -6,8 +6,6 @@ n="$CPU_COUNT" ./configure \ --prefix="$PREFIX" \ - --with-zlib="$PREFIX" \ - --with-libcurl="$PREFIX" \ CPPFLAGS="-I$PREFIX/include" \ LDFLAGS="-Wl,-rpath-link,$PREFIX/lib -Wl,--disable-new-dtags -L$PREFIX/lib" diff --git a/recipes/io_lib/1.14.11/meta.yaml b/recipes/io_lib/1.14.11/meta.yaml index eb902558..b9b2937a 100644 --- a/recipes/io_lib/1.14.11/meta.yaml +++ b/recipes/io_lib/1.14.11/meta.yaml @@ -11,7 +11,7 @@ about: summary: DNA sequence assembly, editing and analysis tools. build: - number: 1 + number: 2 source: url: https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-14-11/io_lib-{{ version }}.tar.gz diff --git a/recipes/io_lib/1.14.9/build.sh b/recipes/io_lib/1.14.9/build.sh index 8a5e46cd..8a151372 100755 --- a/recipes/io_lib/1.14.9/build.sh +++ b/recipes/io_lib/1.14.9/build.sh @@ -6,8 +6,6 @@ n="$CPU_COUNT" ./configure \ --prefix="$PREFIX" \ - --with-zlib="$PREFIX" \ - --with-libcurl="$PREFIX" \ CPPFLAGS="-I$PREFIX/include" \ LDFLAGS="-Wl,-rpath-link,$PREFIX/lib -Wl,--disable-new-dtags -L$PREFIX/lib" diff --git a/recipes/io_lib/1.14.9/meta.yaml b/recipes/io_lib/1.14.9/meta.yaml index 7c686c99..4ec793e5 100644 --- a/recipes/io_lib/1.14.9/meta.yaml +++ b/recipes/io_lib/1.14.9/meta.yaml @@ -11,7 +11,7 @@ about: summary: DNA sequence assembly, editing and analysis tools. build: - number: 0 + number: 1 source: url: https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-14-9/io_lib-{{ version }}.tar.gz From abe2d34701aa14a9fcdd8eda7a723587a5b20a62 Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Tue, 11 Jun 2019 15:38:16 +0100 Subject: [PATCH 095/119] force specific version of htslib for bcftools@1.8 --- recipes/bcftools/1.8/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/bcftools/1.8/meta.yaml b/recipes/bcftools/1.8/meta.yaml index 49753228..cc1c4122 100644 --- a/recipes/bcftools/1.8/meta.yaml +++ b/recipes/bcftools/1.8/meta.yaml @@ -1,5 +1,6 @@ {% set version = "1.8" %} {% set sha256 = "4acbfd691f137742e0be63d09f516434f0faf617a5c60f466140e0677915fced" %} +{% set htslib_version = "1.9+66_gbcf9bff" %} package: name: bcftools @@ -11,8 +12,8 @@ about: summary: C library for high-throughput sequencing data formats. build: - number: 0 - + number: 1 + source: url: https://github.com/samtools/bcftools/releases/download/{{ version }}/bcftools-{{ version }}.tar.bz2 fn: bcftools-{{ version }}.tar.bz2 @@ -21,7 +22,7 @@ source: requirements: build: - gcc_npg >=7.3 - - htslib =={{ version }} + - htslib =={{ htslib_version }} run: - - htslib =={{ version }} + - htslib =={{ htslib_version }} From 8e48c641c6a4d8087673e0ea74c49325f7b1218e Mon Sep 17 00:00:00 2001 From: Kevin Lewis Date: Mon, 1 Jul 2019 17:03:34 +0100 Subject: [PATCH 096/119] recipe for bambi 0.12.1 --- recipes/bambi/0.12.1/build.sh | 12 ++++++++++++ recipes/bambi/0.12.1/meta.yaml | 35 ++++++++++++++++++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100755 recipes/bambi/0.12.1/build.sh create mode 100644 recipes/bambi/0.12.1/meta.yaml diff --git a/recipes/bambi/0.12.1/build.sh b/recipes/bambi/0.12.1/build.sh new file mode 100755 index 00000000..1a1c597a --- /dev/null +++ b/recipes/bambi/0.12.1/build.sh @@ -0,0 +1,12 @@ +#!/bin/sh + +set -e + +autoreconf -fi + +n=`expr $CPU_COUNT / 4 \| 1` + +./configure --prefix="$PREFIX" --with-htslib="$PREFIX" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" + +make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make install prefix="$PREFIX" diff --git a/recipes/bambi/0.12.1/meta.yaml b/recipes/bambi/0.12.1/meta.yaml new file mode 100644 index 00000000..c77aec09 --- /dev/null +++ b/recipes/bambi/0.12.1/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.12.1" %} +{% set htslib_version = "1.9+66_gbcf9bff" %} + + +package: + name: bambi + version: "{{ version }}" + +about: + home: https://github.com/wtsi-npg/bambi + license: AGPL + summary: "A set of programs to manipulate SAM/BAM/CRAM files, using HTSLIB." + +build: + number: 0 + +source: + git_url: https://github.com/wtsi-npg/bambi.git + git_rev: 0.12.1 + +requirements: + build: + - gcc_npg >=7.3 + - htslib =={{ htslib_version }} + - libgd + - libxml2 + + run: + - htslib =={{ htslib_version }} + - libgd + - libxml2 + +test: + commands: + - bambi --version From 0584679b33e6c8428f3622190406c9dd2ed6701b Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Mon, 29 Jul 2019 11:39:01 +0000 Subject: [PATCH 097/119] add bambi 0.12.1 --- recipes/bambi/0.12.1/build.sh | 13 +++++++++++ recipes/bambi/0.12.1/meta.yaml | 41 ++++++++++++++++++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100755 recipes/bambi/0.12.1/build.sh create mode 100644 recipes/bambi/0.12.1/meta.yaml diff --git a/recipes/bambi/0.12.1/build.sh b/recipes/bambi/0.12.1/build.sh new file mode 100755 index 00000000..0deb559a --- /dev/null +++ b/recipes/bambi/0.12.1/build.sh @@ -0,0 +1,13 @@ +#!/bin/sh + +set -ex + +autoreconf -fi + +n="$CPU_COUNT" + +CPPFLAGS="-I$PREFIX/include" LDFLAGS="-Wl,-rpath,$PREFIX/lib -L$PREFIX/lib" \ + ./configure --prefix="$PREFIX" --with-htslib="$PREFIX" + +make -j $n CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make install prefix="$PREFIX" diff --git a/recipes/bambi/0.12.1/meta.yaml b/recipes/bambi/0.12.1/meta.yaml new file mode 100644 index 00000000..67a5d9fb --- /dev/null +++ b/recipes/bambi/0.12.1/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "0.12.1" %} +{% set htslib_version = "1.9+66_gbcf9bff" %} + +package: + name: bambi + version: "{{ version }}" + +about: + home: https://github.com/wtsi-npg/bambi + license: AGPL + summary: "A set of programs to manipulate SAM/BAM/CRAM files, using HTSLIB." + +build: + number: 0 + +source: + git_url: https://github.com/wtsi-npg/bambi.git + git_rev: 0.12.1 + +requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + - pkg-config + host: + - libgd-dev + - libhts-dev =={{ htslib_version }} + - libxml2-dev + - libz-dev + run: + - libgd + - libhts =={{ htslib_version }} + - libxml2 + - libz + +test: + commands: + - bambi --version From 3c1c01d945b9c89e1a53c0175882aa9796e4a7b3 Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 29 Jul 2019 15:33:15 +0100 Subject: [PATCH 098/119] Renamed packages according to the new agreed scheme. --- README.md | 20 +++++++++++++++++++- recipes/baton/1.1.0/meta.yaml | 6 +++--- recipes/bzip2/1.0.6/meta.yaml | 6 +++--- recipes/curl/7.58.0/meta.yaml | 6 +++--- recipes/gnutls/3.4.17/meta.yaml | 6 +++--- recipes/hdf5/1.10.1/meta.yaml | 6 +++--- recipes/htslib/1.9+47-gc93b673/meta.yaml | 9 +++------ recipes/htslib/1.9+66_gbcf9bff/meta.yaml | 9 +++------ recipes/htslib/1.9+9-g6ec3b94/meta.yaml | 9 +++------ recipes/io_lib/1.14.11/meta.yaml | 6 +++--- recipes/io_lib/1.14.9/meta.yaml | 6 +++--- recipes/nettle/3.3/meta.yaml | 6 +++--- recipes/openssl/1.0.2o/meta.yaml | 6 +++--- recipes/pcre/8.41/meta.yaml | 6 +++--- recipes/samtools/1.9+2-g02d93a1/meta.yaml | 6 +++--- recipes/samtools/1.9+37-g5708485/meta.yaml | 6 +++--- recipes/samtools/1.9+48-g2d4907c/meta.yaml | 6 +++--- recipes/xz/5.2.3/meta.yaml | 4 ++-- 18 files changed, 69 insertions(+), 60 deletions(-) diff --git a/README.md b/README.md index e57d7a34..2f43c3d8 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ needs: * Build artefacts are separated into sub-packages. For a typical package written in C and named `example`, these would be: - * `example-bin` containing executables and their documentation, such + * `example` containing executables and their documentation, such as manpages. * `libexample` containing the example libraries (static and shared). @@ -66,3 +66,21 @@ The list of recipe paths may be passed directly to `conda-build`: which will build everything using just the Anaconda defaults channel and the local channel for dependencies. + + +### Naming new recipes ### + +The rules are: + +1. The package containing the executables should be named after the +commonly used name for the software (e.g. bwa, minimap2, curl) + +2. If 1. is not possible e.g. because the executables are in +sub-package, the Conda meta-package is renamed [package name]-pkg and +the executables sub-package keeps the common name +(e.g. curl-pkg,curl,libcurl,libcurl-dev) + +3. If 2. is not possible because e.g. the common name for the software +is a library name and the software also provides executables then the +executables package is renamed [package]-bin +(e.g. libml2-pkg,libxml2-bin,libxml2,libxml2-dev) diff --git a/recipes/baton/1.1.0/meta.yaml b/recipes/baton/1.1.0/meta.yaml index 985d8562..580d45f5 100644 --- a/recipes/baton/1.1.0/meta.yaml +++ b/recipes/baton/1.1.0/meta.yaml @@ -2,7 +2,7 @@ {% set sha256 = "1b8f5711eb04dd2c6f2c423e441054b327138719299864827a6148f127508c5e" %} package: - name: baton + name: baton-pkg version: "{{ version }}" about: @@ -11,7 +11,7 @@ about: summary: Client programs and API for use with iRODS (Integrated Rule-Oriented Data System). build: - number: 2 + number: 3 source: url: https://github.com/wtsi-npg/baton/releases/download/{{ version }}/baton-{{ version }}.tar.gz @@ -38,7 +38,7 @@ requirements: - libssl outputs: - - name: baton-bin + - name: baton version: {{ version }} requirements: build: diff --git a/recipes/bzip2/1.0.6/meta.yaml b/recipes/bzip2/1.0.6/meta.yaml index 5c1f86e2..fbeeea99 100644 --- a/recipes/bzip2/1.0.6/meta.yaml +++ b/recipes/bzip2/1.0.6/meta.yaml @@ -2,7 +2,7 @@ {% set sha256 = "d70a9ccd8bdf47e302d96c69fecd54925f45d9c7b966bb4ef5f56b770960afa7" %} package: - name: bzip2 + name: bzip2-pkg version: "{{ version }}" about: @@ -11,7 +11,7 @@ about: summary: Data compressor. build: - number: 3 + number: 4 source: url: http://http.debian.net/debian/pool/main/b/bzip2/bzip2_{{ version }}.orig.tar.bz2 @@ -27,7 +27,7 @@ requirements: - make outputs: - - name: bzip2-bin + - name: bzip2 version: {{ version }} requirements: build: diff --git a/recipes/curl/7.58.0/meta.yaml b/recipes/curl/7.58.0/meta.yaml index 19fc2fe6..54dcc442 100644 --- a/recipes/curl/7.58.0/meta.yaml +++ b/recipes/curl/7.58.0/meta.yaml @@ -2,7 +2,7 @@ {% set sha256 = "1cb081f97807c01e3ed747b6e1c9fee7a01cb10048f1cd0b5f56cfe0209de731" %} package: - name: curl + name: curl-pkg version: "{{ version }}" about: @@ -11,7 +11,7 @@ about: summary: Command line tool and library for transferring data with URLs. build: - number: 2 + number: 3 source: - url: http://curl.haxx.se/download/curl-{{ version }}.tar.bz2 @@ -31,7 +31,7 @@ requirements: - libz outputs: - - name: curl-bin + - name: curl version: {{ version }} requirements: build: diff --git a/recipes/gnutls/3.4.17/meta.yaml b/recipes/gnutls/3.4.17/meta.yaml index c5bcc0ab..9b40075d 100644 --- a/recipes/gnutls/3.4.17/meta.yaml +++ b/recipes/gnutls/3.4.17/meta.yaml @@ -3,7 +3,7 @@ {% set sha256 = "9b50e8a670d5e950425d96935c7ddd415eb6f8079615a36df425f09a3143172e" %} package: - name: gnutls + name: gnutls-pkg version: "{{ version }}" about: @@ -12,7 +12,7 @@ about: summary: "The GnuTLS Transport Layer Security Library." build: - number: 1 + number: 2 source: - url: https://www.gnupg.org/ftp/gcrypt/gnutls/v{{ short_version }}/gnutls-{{ version }}.tar.xz @@ -35,7 +35,7 @@ requirements: - libz outputs: - - name: gnutls-bin + - name: gnutls version: {{ version }} requirements: build: diff --git a/recipes/hdf5/1.10.1/meta.yaml b/recipes/hdf5/1.10.1/meta.yaml index c28cf5bd..ce2ea8a8 100644 --- a/recipes/hdf5/1.10.1/meta.yaml +++ b/recipes/hdf5/1.10.1/meta.yaml @@ -3,7 +3,7 @@ {% set sha256 = "9c5ce1e33d2463fb1a42dd04daacbc22104e57676e2204e3d66b1ef54b88ebf2" %} package: - name: hdf5 + name: hdf5-pkg version: "{{ version }}" about: @@ -12,7 +12,7 @@ about: summary: A data model, library, and file format for storing and managing data. build: - number: 2 + number: 3 string: threadsafe_{{ PKG_BUILDNUM }} source: @@ -30,7 +30,7 @@ requirements: - libz outputs: - - name: hdf5-bin + - name: hdf5 version: {{ version }} requirements: build: diff --git a/recipes/htslib/1.9+47-gc93b673/meta.yaml b/recipes/htslib/1.9+47-gc93b673/meta.yaml index a2cde097..ff710e44 100644 --- a/recipes/htslib/1.9+47-gc93b673/meta.yaml +++ b/recipes/htslib/1.9+47-gc93b673/meta.yaml @@ -3,7 +3,7 @@ {% set htslib_rev = "c93b6735a8ebddc47a31a325f8c15313d82ae6d5" %} package: - name: "htslib" + name: htslib-pkg version: "{{ version }}" about: @@ -12,7 +12,7 @@ about: summary: C library for high-throughput sequencing data formats. build: - number: 1 + number: 2 string: plugins_{{ plugins_rev }}_{{ PKG_BUILDNUM }} source: @@ -23,9 +23,6 @@ source: git_rev: {{ plugins_rev }} folder: plugins -features: - - irods - requirements: build: - {{ compiler("c") }} @@ -48,7 +45,7 @@ requirements: - libz outputs: - - name: htslib-bin + - name: htslib version: {{ version }} requirements: build: diff --git a/recipes/htslib/1.9+66_gbcf9bff/meta.yaml b/recipes/htslib/1.9+66_gbcf9bff/meta.yaml index 21e932fa..72714f28 100644 --- a/recipes/htslib/1.9+66_gbcf9bff/meta.yaml +++ b/recipes/htslib/1.9+66_gbcf9bff/meta.yaml @@ -3,7 +3,7 @@ {% set htslib_rev = "bcf9bff178f81c9c1cf3a052aeb6cbe32fe5fdcc" %} package: - name: "htslib" + name: htslib-pkg version: "{{ version }}" about: @@ -12,7 +12,7 @@ about: summary: C library for high-throughput sequencing data formats. build: - number: 1 + number: 2 string: plugins_{{ plugins_rev }}_{{ PKG_BUILDNUM }} source: @@ -23,9 +23,6 @@ source: git_rev: {{ plugins_rev }} folder: plugins -features: - - irods - requirements: build: - {{ compiler("c") }} @@ -48,7 +45,7 @@ requirements: - libz outputs: - - name: htslib-bin + - name: htslib version: {{ version }} requirements: build: diff --git a/recipes/htslib/1.9+9-g6ec3b94/meta.yaml b/recipes/htslib/1.9+9-g6ec3b94/meta.yaml index 0cd77d34..13daa0d1 100644 --- a/recipes/htslib/1.9+9-g6ec3b94/meta.yaml +++ b/recipes/htslib/1.9+9-g6ec3b94/meta.yaml @@ -3,7 +3,7 @@ {% set htslib_rev = "6ec3b94d8975e9eb96f0f7b7a2b4c8223d00293a" %} package: - name: "htslib" + name: htslib-pkg version: "{{ version }}" about: @@ -12,7 +12,7 @@ about: summary: C library for high-throughput sequencing data formats. build: - number: 2 + number: 3 string: plugins_{{ plugins_rev }}_{{ PKG_BUILDNUM }} source: @@ -23,9 +23,6 @@ source: git_rev: {{ plugins_rev }} folder: plugins -features: - - irods - requirements: build: - {{ compiler("c") }} @@ -48,7 +45,7 @@ requirements: - libz outputs: - - name: htslib-bin + - name: htslib version: {{ version }} requirements: build: diff --git a/recipes/io_lib/1.14.11/meta.yaml b/recipes/io_lib/1.14.11/meta.yaml index b9b2937a..e2494122 100644 --- a/recipes/io_lib/1.14.11/meta.yaml +++ b/recipes/io_lib/1.14.11/meta.yaml @@ -2,7 +2,7 @@ {% set sha256 = "a172cb66416794fdd9c1fc443f722f7e3439b52c99510b9a60f828392b9989e4" %} package: - name: io_lib + name: io_lib-pkg version: "{{ version }}" about: @@ -11,7 +11,7 @@ about: summary: DNA sequence assembly, editing and analysis tools. build: - number: 2 + number: 3 source: url: https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-14-11/io_lib-{{ version }}.tar.gz @@ -36,7 +36,7 @@ requirements: - libz outputs: - - name: io_lib-bin + - name: io_lib version: {{ version }} requirements: build: diff --git a/recipes/io_lib/1.14.9/meta.yaml b/recipes/io_lib/1.14.9/meta.yaml index 4ec793e5..0ed81ef1 100644 --- a/recipes/io_lib/1.14.9/meta.yaml +++ b/recipes/io_lib/1.14.9/meta.yaml @@ -2,7 +2,7 @@ {% set sha256 = "8d0732f3d37abba1633731bfacac5fd7f8172eccb1cef224e8ced904d3b242f4" %} package: - name: io_lib + name: io_lib-pkg version: "{{ version }}" about: @@ -11,7 +11,7 @@ about: summary: DNA sequence assembly, editing and analysis tools. build: - number: 1 + number: 2 source: url: https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-14-9/io_lib-{{ version }}.tar.gz @@ -36,7 +36,7 @@ requirements: - libz outputs: - - name: io_lib-bin + - name: io_lib version: {{ version }} requirements: build: diff --git a/recipes/nettle/3.3/meta.yaml b/recipes/nettle/3.3/meta.yaml index 9a537494..8cf2566a 100644 --- a/recipes/nettle/3.3/meta.yaml +++ b/recipes/nettle/3.3/meta.yaml @@ -2,7 +2,7 @@ {% set sha256 = "46942627d5d0ca11720fec18d81fc38f7ef837ea4197c1f630e71ce0d470b11e" %} package: - name: nettle + name: nettle-pkg version: "{{ version }}" about: @@ -11,7 +11,7 @@ about: summary: A low-level cryptographic library build: - number: 3 + number: 4 source: url: https://ftp.gnu.org/gnu/nettle/nettle-{{ version }}.tar.gz @@ -31,7 +31,7 @@ requirements: - libgmp >=6.0 outputs: - - name: nettle-bin + - name: nettle requirements: build: - {{ compiler("c") }} diff --git a/recipes/openssl/1.0.2o/meta.yaml b/recipes/openssl/1.0.2o/meta.yaml index 68a17d68..c8e50a5c 100644 --- a/recipes/openssl/1.0.2o/meta.yaml +++ b/recipes/openssl/1.0.2o/meta.yaml @@ -2,7 +2,7 @@ {% set sha256 = "ec3f5c9714ba0fd45cb4e087301eb1336c317e0d20b575a125050470e8089e4d" %} package: - name: openssl + name: openssl-pkg version: "{{ version }}" about: @@ -11,7 +11,7 @@ about: summary: "Cryptography and SSL/TLS Toolkit." build: - number: 2 + number: 3 source: - url: https://www.openssl.org/source/openssl-{{ version }}.tar.gz @@ -30,7 +30,7 @@ requirements: - libz outputs: - - name: openssl-bin + - name: openssl version: {{ version }} requirements: build: diff --git a/recipes/pcre/8.41/meta.yaml b/recipes/pcre/8.41/meta.yaml index 6da72be3..9d5eefa0 100644 --- a/recipes/pcre/8.41/meta.yaml +++ b/recipes/pcre/8.41/meta.yaml @@ -2,7 +2,7 @@ {% set sha256 = "244838e1f1d14f7e2fa7681b857b3a8566b74215f28133f14a8f5e59241b682c" %} package: - name: pcre + name: pcre-pkg version: "{{ version }}" about: @@ -11,7 +11,7 @@ about: summary: "Perl Compatible Regular Expressions." build: - number: 3 + number: 4 source: url: https://ftp.pcre.org/pub/pcre/pcre-{{ version }}.tar.gz @@ -33,7 +33,7 @@ requirements: - libz outputs: - - name: pcre-bin + - name: pcre version: {{ version }} requirements: build: diff --git a/recipes/samtools/1.9+2-g02d93a1/meta.yaml b/recipes/samtools/1.9+2-g02d93a1/meta.yaml index 2f87c7da..ae47e552 100644 --- a/recipes/samtools/1.9+2-g02d93a1/meta.yaml +++ b/recipes/samtools/1.9+2-g02d93a1/meta.yaml @@ -2,7 +2,7 @@ {% set htslib_version = "1.9+9_g6ec3b94" %} package: - name: samtools + name: samtools-pkg version: "{{ version }}" about: @@ -11,7 +11,7 @@ about: summary: C library for high-throughput sequencing data formats. build: - number: 1 + number: 2 source: git_url: https://github.com/samtools/samtools.git @@ -32,7 +32,7 @@ requirements: - libz outputs: - - name: samtools-bin + - name: samtools version: {{ version }} requirements: build: diff --git a/recipes/samtools/1.9+37-g5708485/meta.yaml b/recipes/samtools/1.9+37-g5708485/meta.yaml index 2e5719cd..9257f128 100644 --- a/recipes/samtools/1.9+37-g5708485/meta.yaml +++ b/recipes/samtools/1.9+37-g5708485/meta.yaml @@ -2,7 +2,7 @@ {% set htslib_version = "1.9+47_gc93b673" %} package: - name: samtools + name: samtools-pkg version: "{{ version }}" about: @@ -11,7 +11,7 @@ about: summary: C library for high-throughput sequencing data formats. build: - number: 1 + number: 2 source: git_url: https://github.com/samtools/samtools.git @@ -32,7 +32,7 @@ requirements: - libz outputs: - - name: samtools-bin + - name: samtools version: {{ version }} requirements: build: diff --git a/recipes/samtools/1.9+48-g2d4907c/meta.yaml b/recipes/samtools/1.9+48-g2d4907c/meta.yaml index 33f38ff5..2d26a1ff 100644 --- a/recipes/samtools/1.9+48-g2d4907c/meta.yaml +++ b/recipes/samtools/1.9+48-g2d4907c/meta.yaml @@ -2,7 +2,7 @@ {% set htslib_version = "1.9+66_gbcf9bff" %} package: - name: samtools + name: samtools-pkg version: "{{ version }}" about: @@ -11,7 +11,7 @@ about: summary: C library for high-throughput sequencing data formats. build: - number: 1 + number: 2 source: git_url: https://github.com/samtools/samtools.git @@ -32,7 +32,7 @@ requirements: - libz outputs: - - name: samtools-bin + - name: samtools version: {{ version }} requirements: build: diff --git a/recipes/xz/5.2.3/meta.yaml b/recipes/xz/5.2.3/meta.yaml index cf76c865..88f3e9af 100644 --- a/recipes/xz/5.2.3/meta.yaml +++ b/recipes/xz/5.2.3/meta.yaml @@ -2,7 +2,7 @@ {% set sha256 = "fd9ca16de1052aac899ad3495ad20dfa906c27b4a5070102a2ec35ca3a4740c1" %} package: - name: xz + name: xz-pkg version: "{{ version }}" about: @@ -11,7 +11,7 @@ about: summary: XZ Utils is free general-purpose data compression software. build: - number: 2 + number: 3 source: url: https://tukaani.org/xz/xz-{{ version }}.tar.bz2 From 80cb306f7108f6268047d6fb6520a4fd90f5e9c3 Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Thu, 1 Aug 2019 14:03:20 +0100 Subject: [PATCH 099/119] add wr 0.19.0 --- recipes/wr/0.19.0/build.sh | 12 ++++++++++++ recipes/wr/0.19.0/meta.yaml | 24 ++++++++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 recipes/wr/0.19.0/build.sh create mode 100644 recipes/wr/0.19.0/meta.yaml diff --git a/recipes/wr/0.19.0/build.sh b/recipes/wr/0.19.0/build.sh new file mode 100644 index 00000000..f093a2c3 --- /dev/null +++ b/recipes/wr/0.19.0/build.sh @@ -0,0 +1,12 @@ +#!/bin/sh + +set -e + +mkdir -p "$PREFIX/bin" +cp wr "$PREFIX/bin/" + +mkdir -p "$PREFIX/etc" +cp wr_config.yml "$PREFIX/etc/" + +mkdir -p "$PREFIX/share/doc/wr" +cp README.md "$PREFIX/share/doc/wr/" diff --git a/recipes/wr/0.19.0/meta.yaml b/recipes/wr/0.19.0/meta.yaml new file mode 100644 index 00000000..bbb3df5e --- /dev/null +++ b/recipes/wr/0.19.0/meta.yaml @@ -0,0 +1,24 @@ +{% set version = "0.19.0" %} +{% set sha256 = "f139c4ec5c5e5a735608236120ec891d4070d092b88f58d21f8fb49693b6dfa1" %} + +package: + name: wr + version: "{{ version }}" + +about: + home: https://github.com/VertebrateResequencing/wr + license: GPLv3 + summary: "High performance Workflow Runner." + +build: + number: 0 + binary_relocation: false + +source: + url: https://github.com/VertebrateResequencing/wr/releases/download/v{{ version }}/wr-linux-x86-64.zip + fn: wr-{{ version }}.zip + sha256: {{ sha256 }} + +test: + commands: + - wr -h From a4fc241f0659247c90ed1e3bfb3e0e062c0ace38 Mon Sep 17 00:00:00 2001 From: Kevin Lewis Date: Mon, 5 Aug 2019 13:50:35 +0100 Subject: [PATCH 100/119] fix libstaden version for libmaus2 and libmaus2 version for biobambam2 --- recipes/biobambam2/2.0.79/meta.yaml | 7 ++++--- recipes/libmaus2/2.0.420/meta.yaml | 7 ++++--- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/recipes/biobambam2/2.0.79/meta.yaml b/recipes/biobambam2/2.0.79/meta.yaml index 9fb980a9..17ec3fce 100644 --- a/recipes/biobambam2/2.0.79/meta.yaml +++ b/recipes/biobambam2/2.0.79/meta.yaml @@ -1,5 +1,6 @@ {% set version = "2.0.79" %} {% set sha256 = "1ff1a8afd8fb9f738c4d293e75fb22202db465936f627ea74bc7eff80a4a1e61" %} +{% set libmaus2_version = "2.0.420" %} package: name: biobambam2 @@ -11,7 +12,7 @@ about: summary: Tools for early stage alignment file processing. build: - number: 1 + number: 2 source: url: https://github.com/gt1/biobambam2/archive/{{ version }}-release-20171006114010.tar.gz @@ -26,12 +27,12 @@ requirements: host: - irods-dev - libgnutls-dev - - libmaus2-dev + - libmaus2-dev =={{ libmaus2_version }} - libnettle-dev - libz-dev run: - libgnutls - - libmaus2 + - libmaus2 =={{ libmaus2_version }} - libnettle - libz diff --git a/recipes/libmaus2/2.0.420/meta.yaml b/recipes/libmaus2/2.0.420/meta.yaml index 176689c1..ef398f35 100644 --- a/recipes/libmaus2/2.0.420/meta.yaml +++ b/recipes/libmaus2/2.0.420/meta.yaml @@ -1,5 +1,6 @@ {% set version = "2.0.420" %} {% set sha256 = "0d28932e363e80b4519b04a512df899189c612a4c097130219d6e0ebbfde2a34" %} +{% set io_lib_version = "1.14.9" %} package: name: libmaus2-pkg @@ -11,7 +12,7 @@ about: summary: Collection of data structures and algorithms. build: - number: 1 + number: 2 source: url: https://github.com/gt1/libmaus2/archive/{{ version }}-release-20171116172420.tar.gz @@ -27,12 +28,12 @@ requirements: - irods-dev - libgnutls-dev - libnettle-dev - - libstaden-read-dev + - libstaden-read-dev =={{ io_lib_version }} - libz-dev run: - libgnutls - libnettle - - libstaden-read + - libstaden-read =={{ io_lib_version }} - libz outputs: From 8575f2ec5a51af272a615a38136a17b63c6f9d8f Mon Sep 17 00:00:00 2001 From: Kevin Lewis Date: Mon, 5 Aug 2019 16:42:39 +0100 Subject: [PATCH 101/119] add README.md files to explain requirement for libstaden-read version consistency between biobambam2 and scramble --- recipes/biobambam2/2.0.79/README.md | 4 ++++ recipes/io_lib/1.14.11/README.md | 4 ++++ recipes/libmaus2/2.0.420/README.md | 4 ++++ 3 files changed, 12 insertions(+) create mode 100644 recipes/biobambam2/2.0.79/README.md create mode 100644 recipes/io_lib/1.14.11/README.md create mode 100644 recipes/libmaus2/2.0.420/README.md diff --git a/recipes/biobambam2/2.0.79/README.md b/recipes/biobambam2/2.0.79/README.md new file mode 100644 index 00000000..976b38c8 --- /dev/null +++ b/recipes/biobambam2/2.0.79/README.md @@ -0,0 +1,4 @@ + +ensure that libmaus2 and scramble are built with a particular version of libstaden-read. These versions need to match because "biobambam [...] won't work with modern io_lib's until it is updated to use the resized structure elements" (see https://github.com/samtools/samtools/issues/980) + +So currently (5Aug2019) biobambam2 2.0.79 requires libmaus2 2.0.420 which requires libstaden-read 1.14.11. diff --git a/recipes/io_lib/1.14.11/README.md b/recipes/io_lib/1.14.11/README.md new file mode 100644 index 00000000..976b38c8 --- /dev/null +++ b/recipes/io_lib/1.14.11/README.md @@ -0,0 +1,4 @@ + +ensure that libmaus2 and scramble are built with a particular version of libstaden-read. These versions need to match because "biobambam [...] won't work with modern io_lib's until it is updated to use the resized structure elements" (see https://github.com/samtools/samtools/issues/980) + +So currently (5Aug2019) biobambam2 2.0.79 requires libmaus2 2.0.420 which requires libstaden-read 1.14.11. diff --git a/recipes/libmaus2/2.0.420/README.md b/recipes/libmaus2/2.0.420/README.md new file mode 100644 index 00000000..976b38c8 --- /dev/null +++ b/recipes/libmaus2/2.0.420/README.md @@ -0,0 +1,4 @@ + +ensure that libmaus2 and scramble are built with a particular version of libstaden-read. These versions need to match because "biobambam [...] won't work with modern io_lib's until it is updated to use the resized structure elements" (see https://github.com/samtools/samtools/issues/980) + +So currently (5Aug2019) biobambam2 2.0.79 requires libmaus2 2.0.420 which requires libstaden-read 1.14.11. From 75aeb7650408087e5ff68a76c68e4f5a73cbcd2c Mon Sep 17 00:00:00 2001 From: Kevin Lewis Date: Tue, 6 Aug 2019 09:37:15 +0100 Subject: [PATCH 102/119] add version requirement specification for libstaden-read to outputs section of recipe for libmaus2 create ChangeLog, remove multiple copies of identical README.md for libmaus2, io_lib and biobambam2 --- ChangeLog | 5 +++++ recipes/biobambam2/2.0.79/README.md | 4 ---- recipes/io_lib/1.14.11/README.md | 4 ---- recipes/libmaus2/2.0.420/README.md | 4 ---- recipes/libmaus2/2.0.420/meta.yaml | 4 ++-- 5 files changed, 7 insertions(+), 14 deletions(-) create mode 100644 ChangeLog delete mode 100644 recipes/biobambam2/2.0.79/README.md delete mode 100644 recipes/io_lib/1.14.11/README.md delete mode 100644 recipes/libmaus2/2.0.420/README.md diff --git a/ChangeLog b/ChangeLog new file mode 100644 index 00000000..817ddf9b --- /dev/null +++ b/ChangeLog @@ -0,0 +1,5 @@ + +ensure that libmaus2 and scramble are built with a particular version of libstaden-read. These versions need to match +because "biobambam [...] won't work with modern io_lib's until it is updated to use the resized structure elements" +(see https://github.com/samtools/samtools/issues/980). So currently (5Aug2019) biobambam2 2.0.79 requires +libmaus2 2.0.420 which requires libstaden-read 1.14.9. diff --git a/recipes/biobambam2/2.0.79/README.md b/recipes/biobambam2/2.0.79/README.md deleted file mode 100644 index 976b38c8..00000000 --- a/recipes/biobambam2/2.0.79/README.md +++ /dev/null @@ -1,4 +0,0 @@ - -ensure that libmaus2 and scramble are built with a particular version of libstaden-read. These versions need to match because "biobambam [...] won't work with modern io_lib's until it is updated to use the resized structure elements" (see https://github.com/samtools/samtools/issues/980) - -So currently (5Aug2019) biobambam2 2.0.79 requires libmaus2 2.0.420 which requires libstaden-read 1.14.11. diff --git a/recipes/io_lib/1.14.11/README.md b/recipes/io_lib/1.14.11/README.md deleted file mode 100644 index 976b38c8..00000000 --- a/recipes/io_lib/1.14.11/README.md +++ /dev/null @@ -1,4 +0,0 @@ - -ensure that libmaus2 and scramble are built with a particular version of libstaden-read. These versions need to match because "biobambam [...] won't work with modern io_lib's until it is updated to use the resized structure elements" (see https://github.com/samtools/samtools/issues/980) - -So currently (5Aug2019) biobambam2 2.0.79 requires libmaus2 2.0.420 which requires libstaden-read 1.14.11. diff --git a/recipes/libmaus2/2.0.420/README.md b/recipes/libmaus2/2.0.420/README.md deleted file mode 100644 index 976b38c8..00000000 --- a/recipes/libmaus2/2.0.420/README.md +++ /dev/null @@ -1,4 +0,0 @@ - -ensure that libmaus2 and scramble are built with a particular version of libstaden-read. These versions need to match because "biobambam [...] won't work with modern io_lib's until it is updated to use the resized structure elements" (see https://github.com/samtools/samtools/issues/980) - -So currently (5Aug2019) biobambam2 2.0.79 requires libmaus2 2.0.420 which requires libstaden-read 1.14.11. diff --git a/recipes/libmaus2/2.0.420/meta.yaml b/recipes/libmaus2/2.0.420/meta.yaml index ef398f35..8ef8b70c 100644 --- a/recipes/libmaus2/2.0.420/meta.yaml +++ b/recipes/libmaus2/2.0.420/meta.yaml @@ -48,12 +48,12 @@ outputs: - irods-dev - libgnutls-dev - libnettle-dev - - libstaden-read-dev + - libstaden-read-dev =={{ io_lib_version }} - libz-dev run: - libgnutls - libnettle - - libstaden-read + - libstaden-read =={{ io_lib_version }} - libz files: - lib/libmaus*.* From c27f6953222e4c56fb2f785948c2b809d01d898f Mon Sep 17 00:00:00 2001 From: "David K. Jackson" Date: Tue, 20 Aug 2019 20:03:17 +0000 Subject: [PATCH 103/119] add htslib/1.9+297_g66c41e2 --- recipes/htslib/1.9+297_g66c41e2/build.sh | 27 +++++ recipes/htslib/1.9+297_g66c41e2/meta.yaml | 122 ++++++++++++++++++++++ 2 files changed, 149 insertions(+) create mode 100755 recipes/htslib/1.9+297_g66c41e2/build.sh create mode 100644 recipes/htslib/1.9+297_g66c41e2/meta.yaml diff --git a/recipes/htslib/1.9+297_g66c41e2/build.sh b/recipes/htslib/1.9+297_g66c41e2/build.sh new file mode 100755 index 00000000..95871e80 --- /dev/null +++ b/recipes/htslib/1.9+297_g66c41e2/build.sh @@ -0,0 +1,27 @@ +#!/bin/sh + +set -ex + +n="$CPU_COUNT" + +pushd htslib + +cp aclocal.m4 aclocal.m4.tmp +autoreconf +cp aclocal.m4.tmp aclocal.m4 + +./configure \ + --prefix="$PREFIX" \ + --enable-libcurl \ + --enable-plugins \ + CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" + +make -j $n AR="$AR" +make install prefix="$PREFIX" +popd + +pushd plugins +make IRODS_HOME="$PREFIX" \ + CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make install prefix="$PREFIX" +popd diff --git a/recipes/htslib/1.9+297_g66c41e2/meta.yaml b/recipes/htslib/1.9+297_g66c41e2/meta.yaml new file mode 100644 index 00000000..d3af6b80 --- /dev/null +++ b/recipes/htslib/1.9+297_g66c41e2/meta.yaml @@ -0,0 +1,122 @@ +{% set version = "1.9+297_g66c41e2" %} +{% set plugins_rev = "201712" %} +{% set htslib_rev = "66c41e2c5c563d1a3a7d61883a3012655122e1cb" %} + +package: + name: htslib-pkg + version: "{{ version }}" + +about: + home: https://github.com/samtools/htslib + license: MIT + summary: C library for high-throughput sequencing data formats. + +build: + number: 1 + string: plugins_{{ plugins_rev }}_{{ PKG_BUILDNUM }} + +source: + - git_url: https://github.com/samtools/htslib.git + git_rev: {{ htslib_rev }} + folder: htslib + - git_url: https://github.com/samtools/htslib-plugins.git + git_rev: {{ plugins_rev }} + folder: plugins + +requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - irods-dev >=4.1.12 + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libssl-dev + - libz-dev + run: + - libbz2 + - libcurl + - liblzma + - libssl + - libz + +outputs: + - name: htslib + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - irods-dev >=4.1.12 + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libssl-dev + - libz-dev + run: + - {{ pin_subpackage("libhts", exact=True) }} + - libbz2 + - libcurl + - liblzma + - libssl + - libz + files: + - bin/bgzip + - bin/htsfile + - bin/tabix + - share/man/man1/htsfile.1 + - share/man/man1/tabix.1 + + - name: libhts + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - irods-dev >=4.1.12 + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libssl-dev + - libz-dev + run: + - libbz2 + - libcurl + - liblzma + - libssl + - libz + files: + - libexec/htslib + - lib/libhts* + test: + commands: + - test -f ${PREFIX}/lib/libhts.a + - test -h ${PREFIX}/lib/libhts.so + - test -f ${PREFIX}/libexec/htslib/hfile_irods.so + - test -f ${PREFIX}/libexec/htslib/hfile_libcurl.so + + - name: libhts-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libhts", exact=True) }} + files: + - include/htslib + - share/man/man5/faidx.5 + - share/man/man5/sam.5 + - share/man/man5/vcf.5 + test: + commands: + - test -f ${PREFIX}/include/htslib/sam.h From d397c252648605f0a2913350ab66a4e250771288 Mon Sep 17 00:00:00 2001 From: "David K. Jackson" Date: Tue, 20 Aug 2019 20:26:30 +0000 Subject: [PATCH 104/119] add samtools/1.9+128_g7eb338f --- recipes/samtools/1.9+128_g7eb338f/README.md | 2 + recipes/samtools/1.9+128_g7eb338f/build.sh | 19 ++++++ recipes/samtools/1.9+128_g7eb338f/meta.yaml | 75 +++++++++++++++++++++ 3 files changed, 96 insertions(+) create mode 100644 recipes/samtools/1.9+128_g7eb338f/README.md create mode 100755 recipes/samtools/1.9+128_g7eb338f/build.sh create mode 100644 recipes/samtools/1.9+128_g7eb338f/meta.yaml diff --git a/recipes/samtools/1.9+128_g7eb338f/README.md b/recipes/samtools/1.9+128_g7eb338f/README.md new file mode 100644 index 00000000..19b641b3 --- /dev/null +++ b/recipes/samtools/1.9+128_g7eb338f/README.md @@ -0,0 +1,2 @@ +This post release build was created from the develop branch of +samtools to include the most recent fixes and enhancements. diff --git a/recipes/samtools/1.9+128_g7eb338f/build.sh b/recipes/samtools/1.9+128_g7eb338f/build.sh new file mode 100755 index 00000000..dfa64c6d --- /dev/null +++ b/recipes/samtools/1.9+128_g7eb338f/build.sh @@ -0,0 +1,19 @@ +#!/bin/sh + +set -ex + +n="$CPU_COUNT" + +autoreconf + +./configure --prefix="$PREFIX" \ + --with-htslib=system \ + --without-curses \ + CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" + +make -j "$n" AR="$AR" +make install prefix="$PREFIX" + +mkdir p "$PREFIX/include/samtools" +cp "$SRC_DIR/"*.h "$PREFIX/include/samtools/" +cp "$SRC_DIR/libbam.a" "$PREFIX/lib" diff --git a/recipes/samtools/1.9+128_g7eb338f/meta.yaml b/recipes/samtools/1.9+128_g7eb338f/meta.yaml new file mode 100644 index 00000000..0c1bcb2d --- /dev/null +++ b/recipes/samtools/1.9+128_g7eb338f/meta.yaml @@ -0,0 +1,75 @@ +{% set version = "1.9+128_g7eb338f" %} +{% set htslib_version = "1.9+297_g66c41e2" %} + +package: + name: samtools-pkg + version: "{{ version }}" + +about: + home: https://github.com/samtools/samtools + license: MIT + summary: C library for high-throughput sequencing data formats. + +build: + number: 1 + +source: + git_url: https://github.com/samtools/samtools.git + git_rev: 2d4907cf9a34ccf7cde60143158b39e1cb40ac0c + +requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - libhts-dev =={{ htslib_version }} + - libz-dev + run: + - libhts =={{ htslib_version }} + - libz + +outputs: + - name: samtools + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - libhts-dev =={{ htslib_version }} + - libz-dev + run: + - libhts =={{ htslib_version }} + - libz + files: + - bin/ace2sam + - bin/maq2sam-* + - bin/md5* + - bin/plot-bamstats + - bin/samtools + - bin/wgsim + - bin/*.pl + - bin/*.py + test: + commands: + - echo '@HD VN:1.0 SO:coordinate' | samtools view + + - name: samtools-dev + version: {{ version }} + requirements: + run: + - libhts =={{ htslib_version }} + - libz + files: + - include/samtools/*.h + - lib/libbam.a + test: + commands: + - test -f ${PREFIX}/include/samtools/sam.h + - test -f ${PREFIX}/lib/libbam.a From 9ecccecda4cce49c0e118ee500ec892f19b4ea9d Mon Sep 17 00:00:00 2001 From: "David K. Jackson" Date: Fri, 23 Aug 2019 14:55:46 +0000 Subject: [PATCH 105/119] add gatk 4.1.3.0 --- recipes/gatk/4.1.3.0/build.sh | 16 ++++++++++++++++ recipes/gatk/4.1.3.0/meta.yaml | 24 ++++++++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100755 recipes/gatk/4.1.3.0/build.sh create mode 100644 recipes/gatk/4.1.3.0/meta.yaml diff --git a/recipes/gatk/4.1.3.0/build.sh b/recipes/gatk/4.1.3.0/build.sh new file mode 100755 index 00000000..b95492cc --- /dev/null +++ b/recipes/gatk/4.1.3.0/build.sh @@ -0,0 +1,16 @@ +#!/bin/bash + +BINARY_HOME=$PREFIX/bin +PACKAGE_HOME=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM + +mkdir -p $PREFIX/bin +mkdir -p $PACKAGE_HOME + +sed -i.bak 's#!/usr/bin/env python#!/opt/anaconda1anaconda2anaconda3/bin/python#' gatk +chmod +x gatk +cp gatk ${PACKAGE_HOME}/gatk +cp gatk-*-local.jar $PACKAGE_HOME +# Does not install the spark jars, this is done in the `build_spark.sh` + +ln -s $PACKAGE_HOME/gatk $PREFIX/bin + diff --git a/recipes/gatk/4.1.3.0/meta.yaml b/recipes/gatk/4.1.3.0/meta.yaml new file mode 100644 index 00000000..52aa7ead --- /dev/null +++ b/recipes/gatk/4.1.3.0/meta.yaml @@ -0,0 +1,24 @@ +{% set version = "4.1.3.0" %} +{% set sha256 = "56fd4f03b15a8a01eaa4629f62e3ab15e4d4b957c787efd2d5629b2658c3df0a" %} + +package: + name: gatk + version: "{{ version }}" + +about: + home: https://www.broadinstitute.org/gatk/ + license: BSD-3-Clause + summary: "Genome Analysis Toolkit (GATK4)" + +build: + number: 0 + +source: + url: https://github.com/broadinstitute/gatk/releases/download/{{ version }}/gatk-{{ version }}.zip + sha256: {{ sha256 }} + +requirements: + run: + - openjdk >=8,<9 + - python + From d55bc47da61f1cbc3bc3289af3f5a5358b7fce7f Mon Sep 17 00:00:00 2001 From: "David K. Jackson" Date: Sat, 24 Aug 2019 22:07:31 +0000 Subject: [PATCH 106/119] add libdeflate (and use in htslib) --- recipes/htslib/1.9+297_g66c41e2/build.sh | 3 ++ recipes/htslib/1.9+297_g66c41e2/meta.yaml | 13 ++++-- recipes/libdeflate/1.3/build.sh | 9 ++++ recipes/libdeflate/1.3/meta.yaml | 56 +++++++++++++++++++++++ 4 files changed, 78 insertions(+), 3 deletions(-) create mode 100755 recipes/libdeflate/1.3/build.sh create mode 100644 recipes/libdeflate/1.3/meta.yaml diff --git a/recipes/htslib/1.9+297_g66c41e2/build.sh b/recipes/htslib/1.9+297_g66c41e2/build.sh index 95871e80..a5c7ee3e 100755 --- a/recipes/htslib/1.9+297_g66c41e2/build.sh +++ b/recipes/htslib/1.9+297_g66c41e2/build.sh @@ -12,7 +12,10 @@ cp aclocal.m4.tmp aclocal.m4 ./configure \ --prefix="$PREFIX" \ + --with-libdeflate \ --enable-libcurl \ + --enable-s3 \ + --enable-gcs \ --enable-plugins \ CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" diff --git a/recipes/htslib/1.9+297_g66c41e2/meta.yaml b/recipes/htslib/1.9+297_g66c41e2/meta.yaml index d3af6b80..85a0ce87 100644 --- a/recipes/htslib/1.9+297_g66c41e2/meta.yaml +++ b/recipes/htslib/1.9+297_g66c41e2/meta.yaml @@ -12,7 +12,7 @@ about: summary: C library for high-throughput sequencing data formats. build: - number: 1 + number: 2 string: plugins_{{ plugins_rev }}_{{ PKG_BUILDNUM }} source: @@ -34,12 +34,14 @@ requirements: - irods-dev >=4.1.12 - libbz2-dev - libcurl-dev + - libdeflate-dev - liblzma-dev - libssl-dev - libz-dev run: - libbz2 - libcurl + - libdeflate - liblzma - libssl - libz @@ -58,6 +60,7 @@ outputs: - irods-dev >=4.1.12 - libbz2-dev - libcurl-dev + - libdeflate-dev - liblzma-dev - libssl-dev - libz-dev @@ -65,6 +68,7 @@ outputs: - {{ pin_subpackage("libhts", exact=True) }} - libbz2 - libcurl + - libdeflate - liblzma - libssl - libz @@ -88,21 +92,22 @@ outputs: - irods-dev >=4.1.12 - libbz2-dev - libcurl-dev + - libdeflate-dev - liblzma-dev - libssl-dev - libz-dev run: - libbz2 - libcurl + - libdeflate - liblzma - libssl - libz files: - libexec/htslib - - lib/libhts* + - lib/libhts.so* test: commands: - - test -f ${PREFIX}/lib/libhts.a - test -h ${PREFIX}/lib/libhts.so - test -f ${PREFIX}/libexec/htslib/hfile_irods.so - test -f ${PREFIX}/libexec/htslib/hfile_libcurl.so @@ -114,9 +119,11 @@ outputs: - {{ pin_subpackage("libhts", exact=True) }} files: - include/htslib + - lib/libhts.a - share/man/man5/faidx.5 - share/man/man5/sam.5 - share/man/man5/vcf.5 test: commands: + - test -f ${PREFIX}/lib/libhts.a - test -f ${PREFIX}/include/htslib/sam.h diff --git a/recipes/libdeflate/1.3/build.sh b/recipes/libdeflate/1.3/build.sh new file mode 100755 index 00000000..4db08ac0 --- /dev/null +++ b/recipes/libdeflate/1.3/build.sh @@ -0,0 +1,9 @@ +#!/bin/sh + +set -ex + +n="$CPU_COUNT" + +make -j $n +make install PREFIX="$PREFIX" + diff --git a/recipes/libdeflate/1.3/meta.yaml b/recipes/libdeflate/1.3/meta.yaml new file mode 100644 index 00000000..e064b8d7 --- /dev/null +++ b/recipes/libdeflate/1.3/meta.yaml @@ -0,0 +1,56 @@ +{% set version = "1.3" %} +{% set sha256 = "09a23f5a6bf74789605a452364fae2156627a0a62a3de2a82ceb362982a87f0b" %} + +package: + name: libdeflate-pkg + version: "{{ version }}" + +about: + home: https://github.com/ebiggers/libdeflate + license: MIT + summary: >- + Heavily optimized library for DEFLATE/zlib/gzip compression and + decompression. + +source: + url: https://github.com/ebiggers/libdeflate/archive/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - {{ compiler("c") }} + - make + +outputs: + - name: libdeflate + files: + - lib/libdeflate.so* + test: + commands: + - test -h ${PREFIX}/lib/libdeflate.so + - test -f $( readlink -f ${PREFIX}/lib/libdeflate.so ) + + - name: libdeflate-dev + files: + - include/libdeflate.h + - lib/libdeflate.a + requirements: + run: + - {{ pin_subpackage("libdeflate", exact=True) }} + test: + commands: + - test -f ${PREFIX}/include/libdeflate.h + - test -f ${PREFIX}/lib/libdeflate.a + + - name: libdeflate-bin + files: + - bin/libdeflate-gzip + - bin/libdeflate-gunzip + test: + commands: + - test -f ${PREFIX}/bin/libdeflate-gzip + - test -f ${PREFIX}/bin/libdeflate-gunzip + From 526d263f71dee40615a8d61940eb91e91109cd63 Mon Sep 17 00:00:00 2001 From: "David K. Jackson" Date: Tue, 27 Aug 2019 15:53:07 +0000 Subject: [PATCH 107/119] bcftools 1.9 to use htslib 1.9 --- recipes/bcftools/1.9/meta.yaml | 8 +-- recipes/htslib/1.9/build.sh | 30 ++++++++ recipes/htslib/1.9/meta.yaml | 127 +++++++++++++++++++++++++++++++++ 3 files changed, 161 insertions(+), 4 deletions(-) create mode 100755 recipes/htslib/1.9/build.sh create mode 100644 recipes/htslib/1.9/meta.yaml diff --git a/recipes/bcftools/1.9/meta.yaml b/recipes/bcftools/1.9/meta.yaml index 0fa0d7e1..ec1d8372 100644 --- a/recipes/bcftools/1.9/meta.yaml +++ b/recipes/bcftools/1.9/meta.yaml @@ -1,5 +1,5 @@ {% set version = "1.9" %} -{% set maxversion = "1.10" %} +{% set htslib_version = "1.9" %} {% set sha256 = "6f36d0e6f16ec4acf88649fb1565d443acf0ba40f25a9afd87f14d14d13070c8" %} package: @@ -12,7 +12,7 @@ about: summary: VCF commands and BCF calling. build: - number: 1 + number: 2 source: url: https://github.com/samtools/bcftools/releases/download/{{ version }}/bcftools-{{ version }}.tar.bz2 @@ -24,10 +24,10 @@ requirements: - {{ compiler("c") }} - make host: - - libhts-dev >={{ version }},<{{ maxversion }} + - libhts-dev =={{ htslib_version }} - libz-dev run: - - libhts >={{ version }},<{{ maxversion }} + - libhts =={{ htslib_version }} - libz test: diff --git a/recipes/htslib/1.9/build.sh b/recipes/htslib/1.9/build.sh new file mode 100755 index 00000000..f6526d03 --- /dev/null +++ b/recipes/htslib/1.9/build.sh @@ -0,0 +1,30 @@ +#!/bin/sh + +set -ex + +n="$CPU_COUNT" + +pushd htslib + +cp aclocal.m4 aclocal.m4.tmp || echo no aclocal.m4 +autoreconf +cp aclocal.m4.tmp aclocal.m4 || true + +./configure \ + --prefix="$PREFIX" \ + --prefix="$PREFIX" \ + --enable-libcurl \ + --enable-s3 \ + --enable-gcp \ + --enable-plugins \ + CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" + +make -j $n AR="$AR" +make install prefix="$PREFIX" +popd + +pushd plugins +make IRODS_HOME="$PREFIX" \ + CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make install prefix="$PREFIX" +popd diff --git a/recipes/htslib/1.9/meta.yaml b/recipes/htslib/1.9/meta.yaml new file mode 100644 index 00000000..bb09b463 --- /dev/null +++ b/recipes/htslib/1.9/meta.yaml @@ -0,0 +1,127 @@ +{% set version = "1.9" %} +{% set plugins_rev = "201712" %} +{% set htslib_rev = "1832d3a1b75133e55fb6abffc3f50f8a6ed5ceae" %} + +package: + name: htslib-pkg + version: "{{ version }}" + +about: + home: https://github.com/samtools/htslib + license: MIT + summary: C library for high-throughput sequencing data formats. + +build: + number: 2 + string: plugins_{{ plugins_rev }}_{{ PKG_BUILDNUM }} + +source: + - git_url: https://github.com/samtools/htslib.git + git_rev: {{ htslib_rev }} + folder: htslib + - git_url: https://github.com/samtools/htslib-plugins.git + git_rev: {{ plugins_rev }} + folder: plugins + +requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - irods-dev >=4.1.12 + - libbz2-dev + - libcurl-dev + - libdeflate-dev + - liblzma-dev + - libssl-dev + - libz-dev + run: + - libbz2 + - libcurl + - liblzma + - libssl + - libz + +outputs: + - name: htslib + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - irods-dev >=4.1.12 + - libbz2-dev + - libcurl-dev + - libdeflate-dev + - liblzma-dev + - libssl-dev + - libz-dev + run: + - {{ pin_subpackage("libhts", exact=True) }} + - libbz2 + - libcurl + - libdeflate + - liblzma + - libssl + - libz + files: + - bin/bgzip + - bin/htsfile + - bin/tabix + - share/man/man1/htsfile.1 + - share/man/man1/tabix.1 + + - name: libhts + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - irods-dev >=4.1.12 + - libbz2-dev + - libcurl-dev + - libdeflate-dev + - liblzma-dev + - libssl-dev + - libz-dev + run: + - libbz2 + - libcurl + - libdeflate + - liblzma + - libssl + - libz + files: + - libexec/htslib + - lib/libhts* + test: + commands: + - test -f ${PREFIX}/lib/libhts.a + - test -h ${PREFIX}/lib/libhts.so + - test -f ${PREFIX}/libexec/htslib/hfile_irods.so + - test -f ${PREFIX}/libexec/htslib/hfile_libcurl.so + + - name: libhts-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libhts", exact=True) }} + files: + - include/htslib + - share/man/man5/faidx.5 + - share/man/man5/sam.5 + - share/man/man5/vcf.5 + test: + commands: + - test -f ${PREFIX}/include/htslib/sam.h From 36b41c2174df36fff881047b995ef11ec119e973 Mon Sep 17 00:00:00 2001 From: "David K. Jackson" Date: Tue, 27 Aug 2019 18:34:16 +0000 Subject: [PATCH 108/119] split htslib-plugins into separate conda package (and outputs) --- recipes/htslib-plugins/201712/build.sh | 11 ++++ recipes/htslib-plugins/201712/meta.yaml | 76 +++++++++++++++++++++++ recipes/htslib/1.9+297_g66c41e2/build.sh | 5 -- recipes/htslib/1.9+297_g66c41e2/meta.yaml | 11 +--- 4 files changed, 88 insertions(+), 15 deletions(-) create mode 100755 recipes/htslib-plugins/201712/build.sh create mode 100644 recipes/htslib-plugins/201712/meta.yaml diff --git a/recipes/htslib-plugins/201712/build.sh b/recipes/htslib-plugins/201712/build.sh new file mode 100755 index 00000000..3119b44e --- /dev/null +++ b/recipes/htslib-plugins/201712/build.sh @@ -0,0 +1,11 @@ +#!/bin/sh + +set -ex + +n="$CPU_COUNT" + +pushd plugins +make IRODS_HOME="$PREFIX" \ + CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" +make install prefix="$PREFIX" +popd diff --git a/recipes/htslib-plugins/201712/meta.yaml b/recipes/htslib-plugins/201712/meta.yaml new file mode 100644 index 00000000..4b279f4f --- /dev/null +++ b/recipes/htslib-plugins/201712/meta.yaml @@ -0,0 +1,76 @@ +{% set version = "201712" %} + +package: + name: htslib-plugins + version: "{{ version }}" + +about: + home: https://github.com/samtools/htslib + license: MIT + summary: C library for high-throughput sequencing data formats. + +build: + number: 0 + +source: + - git_url: https://github.com/samtools/htslib-plugins.git + git_rev: {{ version }} + folder: plugins + +requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - irods-dev >=4.1.12 + - libbz2-dev + - libcurl-dev + - libdeflate-dev + - libhts-dev + - liblzma-dev + - libssl-dev + - libz-dev + run: + - libbz2 + - libcurl + - libdeflate + - liblzma + - libssl + - libz + +outputs: + - name: libhts-plugins + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - irods-dev >=4.1.12 + - libbz2-dev + - libcurl-dev + - libdeflate-dev + - libhts-dev + - liblzma-dev + - libssl-dev + - libz-dev + run: + - libbz2 + - libcurl + - libdeflate + - libhts + - liblzma + - libssl + - libz + files: + - libexec/htslib/hfile_irods.so + - libexec/htslib/hfile_mmap.so + test: + commands: + - test -f ${PREFIX}/libexec/htslib/hfile_irods.so diff --git a/recipes/htslib/1.9+297_g66c41e2/build.sh b/recipes/htslib/1.9+297_g66c41e2/build.sh index a5c7ee3e..527de7c9 100755 --- a/recipes/htslib/1.9+297_g66c41e2/build.sh +++ b/recipes/htslib/1.9+297_g66c41e2/build.sh @@ -23,8 +23,3 @@ make -j $n AR="$AR" make install prefix="$PREFIX" popd -pushd plugins -make IRODS_HOME="$PREFIX" \ - CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" -make install prefix="$PREFIX" -popd diff --git a/recipes/htslib/1.9+297_g66c41e2/meta.yaml b/recipes/htslib/1.9+297_g66c41e2/meta.yaml index 85a0ce87..a7aaf9dd 100644 --- a/recipes/htslib/1.9+297_g66c41e2/meta.yaml +++ b/recipes/htslib/1.9+297_g66c41e2/meta.yaml @@ -1,5 +1,4 @@ {% set version = "1.9+297_g66c41e2" %} -{% set plugins_rev = "201712" %} {% set htslib_rev = "66c41e2c5c563d1a3a7d61883a3012655122e1cb" %} package: @@ -12,16 +11,12 @@ about: summary: C library for high-throughput sequencing data formats. build: - number: 2 - string: plugins_{{ plugins_rev }}_{{ PKG_BUILDNUM }} + number: 3 source: - git_url: https://github.com/samtools/htslib.git git_rev: {{ htslib_rev }} folder: htslib - - git_url: https://github.com/samtools/htslib-plugins.git - git_rev: {{ plugins_rev }} - folder: plugins requirements: build: @@ -31,7 +26,6 @@ requirements: - make - perl host: - - irods-dev >=4.1.12 - libbz2-dev - libcurl-dev - libdeflate-dev @@ -57,7 +51,6 @@ outputs: - make - perl host: - - irods-dev >=4.1.12 - libbz2-dev - libcurl-dev - libdeflate-dev @@ -89,7 +82,6 @@ outputs: - make - perl host: - - irods-dev >=4.1.12 - libbz2-dev - libcurl-dev - libdeflate-dev @@ -109,7 +101,6 @@ outputs: test: commands: - test -h ${PREFIX}/lib/libhts.so - - test -f ${PREFIX}/libexec/htslib/hfile_irods.so - test -f ${PREFIX}/libexec/htslib/hfile_libcurl.so - name: libhts-dev From b5d424defbac7786b8dfe624117e8641d8ff92c0 Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 27 Aug 2019 16:02:34 +0100 Subject: [PATCH 109/119] Improved error reporting on build failure. The "run" method is preferred now, in Python3. Now captures STDOUT and STDERR, decodes bytes with the defined system encoding (rather than hard-coding UTF-8) and book-ends the messages with some easy-to-find delimiters. --- scripts/build.py | 19 ++++++++++++++----- 1 file changed, 14 insertions(+), 5 deletions(-) diff --git a/scripts/build.py b/scripts/build.py index 6838ce6b..86114515 100755 --- a/scripts/build.py +++ b/scripts/build.py @@ -170,13 +170,22 @@ def docker_pull(image): log.debug('Build script: "%s"', build_script) try: - output = subprocess.check_output(cmd, stderr=subprocess.STDOUT) - for line in output.decode("utf-8").split("\n"): - log.debug(line) + enc = sys.getfilesystemencoding() + + # Combine STDOUT and STDERR + output = subprocess.run(cmd, check=True, + stdout=subprocess.PIPE, + stderr=subprocess.STDOUT) + log.debug("########## BEGIN process STDOUT/STDERR ##########") + for outline in output.stdout.decode(enc).split("\n"): + log.debug(outline) + log.debug("########## END process STDOUT/STDERR ##########") except subprocess.CalledProcessError as e: fail = True - for line in e.output.decode("utf-8").split("\n"): - log.error(line) + log.error("########## BEGIN process STDOUT/STDERR ##########") + for errline in e.stdout.decode(enc).split("\n"): + log.error(errline) + log.error("########## END process STDOUT/STDERR ##########") if fail: exit(1) From 05467aaef6caf39086c248cf021b1190b4783842 Mon Sep 17 00:00:00 2001 From: "David K. Jackson" Date: Thu, 29 Aug 2019 11:56:12 +0000 Subject: [PATCH 110/119] add hdf5-all package to pull in hdf5, libhdf5 and libhdf5-dev, & static in dev --- recipes/hdf5/1.10.1/meta.yaml | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/recipes/hdf5/1.10.1/meta.yaml b/recipes/hdf5/1.10.1/meta.yaml index ce2ea8a8..f76d7a1f 100644 --- a/recipes/hdf5/1.10.1/meta.yaml +++ b/recipes/hdf5/1.10.1/meta.yaml @@ -12,7 +12,7 @@ about: summary: A data model, library, and file format for storing and managing data. build: - number: 3 + number: 4 string: threadsafe_{{ PKG_BUILDNUM }} source: @@ -30,6 +30,14 @@ requirements: - libz outputs: + - name: hdf5-all + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libhdf5", exact=True) }} + - {{ pin_subpackage("libhdf5-dev", exact=True) }} + - {{ pin_subpackage("hdf5", exact=True) }} + - name: hdf5 version: {{ version }} requirements: @@ -74,10 +82,9 @@ outputs: run: - libz files: - - lib/libhdf* + - lib/libhdf5.so* test: commands: - - test -f ${PREFIX}/lib/libhdf5.a - test -h ${PREFIX}/lib/libhdf5.so - name: libhdf5-dev @@ -86,9 +93,11 @@ outputs: run: - {{ pin_subpackage("libhdf5", exact=True) }} files: + - lib/libhdf5.a - include/H5* - include/hdf5* - share/hdf5_examples test: commands: + - test -f ${PREFIX}/lib/libhdf5.a - test -f ${PREFIX}/include/hdf5.h From 5c4cb9bcce157d758bf55f051ff236410ab75a40 Mon Sep 17 00:00:00 2001 From: "David K. Jackson" Date: Fri, 30 Aug 2019 08:11:14 +0000 Subject: [PATCH 111/119] add htslib/1.9+317_gc31dedd --- recipes/htslib/1.9+317_gc31dedd/build.sh | 25 +++++ recipes/htslib/1.9+317_gc31dedd/meta.yaml | 120 ++++++++++++++++++++++ 2 files changed, 145 insertions(+) create mode 100755 recipes/htslib/1.9+317_gc31dedd/build.sh create mode 100644 recipes/htslib/1.9+317_gc31dedd/meta.yaml diff --git a/recipes/htslib/1.9+317_gc31dedd/build.sh b/recipes/htslib/1.9+317_gc31dedd/build.sh new file mode 100755 index 00000000..527de7c9 --- /dev/null +++ b/recipes/htslib/1.9+317_gc31dedd/build.sh @@ -0,0 +1,25 @@ +#!/bin/sh + +set -ex + +n="$CPU_COUNT" + +pushd htslib + +cp aclocal.m4 aclocal.m4.tmp +autoreconf +cp aclocal.m4.tmp aclocal.m4 + +./configure \ + --prefix="$PREFIX" \ + --with-libdeflate \ + --enable-libcurl \ + --enable-s3 \ + --enable-gcs \ + --enable-plugins \ + CC="$GCC" CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" + +make -j $n AR="$AR" +make install prefix="$PREFIX" +popd + diff --git a/recipes/htslib/1.9+317_gc31dedd/meta.yaml b/recipes/htslib/1.9+317_gc31dedd/meta.yaml new file mode 100644 index 00000000..2ff5d6e5 --- /dev/null +++ b/recipes/htslib/1.9+317_gc31dedd/meta.yaml @@ -0,0 +1,120 @@ +{% set version = "1.9+317_gc31dedd" %} +{% set htslib_rev = "c31dedd7da3fc860543d736551f8375a7d7e5a80" %} + +package: + name: htslib-pkg + version: "{{ version }}" + +about: + home: https://github.com/samtools/htslib + license: MIT + summary: C library for high-throughput sequencing data formats. + +build: + number: 3 + +source: + - git_url: https://github.com/samtools/htslib.git + git_rev: {{ htslib_rev }} + folder: htslib + +requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - libbz2-dev + - libcurl-dev + - libdeflate-dev + - liblzma-dev + - libssl-dev + - libz-dev + run: + - libbz2 + - libcurl + - libdeflate + - liblzma + - libssl + - libz + +outputs: + - name: htslib + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - libbz2-dev + - libcurl-dev + - libdeflate-dev + - liblzma-dev + - libssl-dev + - libz-dev + run: + - {{ pin_subpackage("libhts", exact=True) }} + - libbz2 + - libcurl + - libdeflate + - liblzma + - libssl + - libz + files: + - bin/bgzip + - bin/htsfile + - bin/tabix + - share/man/man1/htsfile.1 + - share/man/man1/tabix.1 + + - name: libhts + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - libbz2-dev + - libcurl-dev + - libdeflate-dev + - liblzma-dev + - libssl-dev + - libz-dev + run: + - libbz2 + - libcurl + - libdeflate + - liblzma + - libssl + - libz + files: + - libexec/htslib + - lib/libhts.so* + test: + commands: + - test -h ${PREFIX}/lib/libhts.so + - test -f ${PREFIX}/libexec/htslib/hfile_libcurl.so + + - name: libhts-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libhts", exact=True) }} + files: + - include/htslib + - lib/libhts.a + - share/man/man5/faidx.5 + - share/man/man5/sam.5 + - share/man/man5/vcf.5 + test: + commands: + - test -f ${PREFIX}/lib/libhts.a + - test -f ${PREFIX}/include/htslib/sam.h From 587537de20bb8a776fae8f97f3c1ac47ffcb64b7 Mon Sep 17 00:00:00 2001 From: "David K. Jackson" Date: Mon, 2 Sep 2019 11:04:51 +0000 Subject: [PATCH 112/119] Samtools with PR 1091 merged to test functional equivalence capability --- recipes/samtools/1.9+154_gc661e69/README.md | 2 + recipes/samtools/1.9+154_gc661e69/build.sh | 19 ++++++ recipes/samtools/1.9+154_gc661e69/meta.yaml | 75 +++++++++++++++++++++ 3 files changed, 96 insertions(+) create mode 100644 recipes/samtools/1.9+154_gc661e69/README.md create mode 100755 recipes/samtools/1.9+154_gc661e69/build.sh create mode 100644 recipes/samtools/1.9+154_gc661e69/meta.yaml diff --git a/recipes/samtools/1.9+154_gc661e69/README.md b/recipes/samtools/1.9+154_gc661e69/README.md new file mode 100644 index 00000000..d8745720 --- /dev/null +++ b/recipes/samtools/1.9+154_gc661e69/README.md @@ -0,0 +1,2 @@ +This post release build was created from the develop branch of +samtools with PR 1091 included. diff --git a/recipes/samtools/1.9+154_gc661e69/build.sh b/recipes/samtools/1.9+154_gc661e69/build.sh new file mode 100755 index 00000000..dfa64c6d --- /dev/null +++ b/recipes/samtools/1.9+154_gc661e69/build.sh @@ -0,0 +1,19 @@ +#!/bin/sh + +set -ex + +n="$CPU_COUNT" + +autoreconf + +./configure --prefix="$PREFIX" \ + --with-htslib=system \ + --without-curses \ + CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" + +make -j "$n" AR="$AR" +make install prefix="$PREFIX" + +mkdir p "$PREFIX/include/samtools" +cp "$SRC_DIR/"*.h "$PREFIX/include/samtools/" +cp "$SRC_DIR/libbam.a" "$PREFIX/lib" diff --git a/recipes/samtools/1.9+154_gc661e69/meta.yaml b/recipes/samtools/1.9+154_gc661e69/meta.yaml new file mode 100644 index 00000000..f67b9f8e --- /dev/null +++ b/recipes/samtools/1.9+154_gc661e69/meta.yaml @@ -0,0 +1,75 @@ +{% set version = "1.9+154_gc661e69" %} +{% set htslib_version = "1.9+297_g66c41e2" %} + +package: + name: samtools-pkg + version: "{{ version }}" + +about: + home: https://github.com/samtools/samtools + license: MIT + summary: C library for high-throughput sequencing data formats. + +build: + number: 1 + +source: + git_url: https://github.com/dkj/samtools.git + git_rev: c661e698b92cf0b15e04675490187dfdb7e4f8df + +requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - libhts-dev =={{ htslib_version }} + - libz-dev + run: + - libhts =={{ htslib_version }} + - libz + +outputs: + - name: samtools + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + - automake + - make + - perl + host: + - libhts-dev =={{ htslib_version }} + - libz-dev + run: + - libhts =={{ htslib_version }} + - libz + files: + - bin/ace2sam + - bin/maq2sam-* + - bin/md5* + - bin/plot-bamstats + - bin/samtools + - bin/wgsim + - bin/*.pl + - bin/*.py + test: + commands: + - echo '@HD VN:1.0 SO:coordinate' | samtools view + + - name: samtools-dev + version: {{ version }} + requirements: + run: + - libhts =={{ htslib_version }} + - libz + files: + - include/samtools/*.h + - lib/libbam.a + test: + commands: + - test -f ${PREFIX}/include/samtools/sam.h + - test -f ${PREFIX}/lib/libbam.a From 640e6832aa7ee8de84ecddd9c8c72ac22731bf10 Mon Sep 17 00:00:00 2001 From: "David K. Jackson" Date: Mon, 2 Sep 2019 11:06:26 +0000 Subject: [PATCH 113/119] Rebase of Samtools with PR 1091 merged to test functional equivalence capability --- .../{1.9+154_gc661e69 => 1.9+160_g8af021c}/README.md | 0 .../{1.9+154_gc661e69 => 1.9+160_g8af021c}/build.sh | 0 .../{1.9+154_gc661e69 => 1.9+160_g8af021c}/meta.yaml | 6 +++--- 3 files changed, 3 insertions(+), 3 deletions(-) rename recipes/samtools/{1.9+154_gc661e69 => 1.9+160_g8af021c}/README.md (100%) rename recipes/samtools/{1.9+154_gc661e69 => 1.9+160_g8af021c}/build.sh (100%) rename recipes/samtools/{1.9+154_gc661e69 => 1.9+160_g8af021c}/meta.yaml (90%) diff --git a/recipes/samtools/1.9+154_gc661e69/README.md b/recipes/samtools/1.9+160_g8af021c/README.md similarity index 100% rename from recipes/samtools/1.9+154_gc661e69/README.md rename to recipes/samtools/1.9+160_g8af021c/README.md diff --git a/recipes/samtools/1.9+154_gc661e69/build.sh b/recipes/samtools/1.9+160_g8af021c/build.sh similarity index 100% rename from recipes/samtools/1.9+154_gc661e69/build.sh rename to recipes/samtools/1.9+160_g8af021c/build.sh diff --git a/recipes/samtools/1.9+154_gc661e69/meta.yaml b/recipes/samtools/1.9+160_g8af021c/meta.yaml similarity index 90% rename from recipes/samtools/1.9+154_gc661e69/meta.yaml rename to recipes/samtools/1.9+160_g8af021c/meta.yaml index f67b9f8e..f349cb3c 100644 --- a/recipes/samtools/1.9+154_gc661e69/meta.yaml +++ b/recipes/samtools/1.9+160_g8af021c/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.9+154_gc661e69" %} -{% set htslib_version = "1.9+297_g66c41e2" %} +{% set version = "1.9+160_g8af021c" %} +{% set htslib_version = "1.9+317_gc31dedd" %} package: name: samtools-pkg @@ -15,7 +15,7 @@ build: source: git_url: https://github.com/dkj/samtools.git - git_rev: c661e698b92cf0b15e04675490187dfdb7e4f8df + git_rev: 8af021c833c876cd4e261ed0f7dfdc740654a81f requirements: build: From 3314bd07d8a00e03d919e4486ea7609893e573f5 Mon Sep 17 00:00:00 2001 From: "David K. Jackson" Date: Mon, 2 Sep 2019 11:18:54 +0000 Subject: [PATCH 114/119] Rename recipe for Samtools with PR 1091 merged to test functional equivalence capability --- recipes/samtools/{1.9+160_g8af021c => 1.9+fealpha}/README.md | 0 recipes/samtools/{1.9+160_g8af021c => 1.9+fealpha}/build.sh | 0 recipes/samtools/{1.9+160_g8af021c => 1.9+fealpha}/meta.yaml | 2 +- 3 files changed, 1 insertion(+), 1 deletion(-) rename recipes/samtools/{1.9+160_g8af021c => 1.9+fealpha}/README.md (100%) rename recipes/samtools/{1.9+160_g8af021c => 1.9+fealpha}/build.sh (100%) rename recipes/samtools/{1.9+160_g8af021c => 1.9+fealpha}/meta.yaml (96%) diff --git a/recipes/samtools/1.9+160_g8af021c/README.md b/recipes/samtools/1.9+fealpha/README.md similarity index 100% rename from recipes/samtools/1.9+160_g8af021c/README.md rename to recipes/samtools/1.9+fealpha/README.md diff --git a/recipes/samtools/1.9+160_g8af021c/build.sh b/recipes/samtools/1.9+fealpha/build.sh similarity index 100% rename from recipes/samtools/1.9+160_g8af021c/build.sh rename to recipes/samtools/1.9+fealpha/build.sh diff --git a/recipes/samtools/1.9+160_g8af021c/meta.yaml b/recipes/samtools/1.9+fealpha/meta.yaml similarity index 96% rename from recipes/samtools/1.9+160_g8af021c/meta.yaml rename to recipes/samtools/1.9+fealpha/meta.yaml index f349cb3c..9fa3f624 100644 --- a/recipes/samtools/1.9+160_g8af021c/meta.yaml +++ b/recipes/samtools/1.9+fealpha/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.9+160_g8af021c" %} +{% set version = "1.9+fealpha_160_g8af021c" %} {% set htslib_version = "1.9+317_gc31dedd" %} package: From fbe4fd7d854d019a4cec4e67bd4e7fe51c837b5b Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 2 Sep 2019 16:36:53 +0100 Subject: [PATCH 115/119] Bugfix: ensure all packages are added to the graph Pakcages having declared requirements all of which are outside of the scope of the dependency tree were omitted from the graph. --- scripts/package_sort.py | 30 +++++++++++++----------------- 1 file changed, 13 insertions(+), 17 deletions(-) diff --git a/scripts/package_sort.py b/scripts/package_sort.py index 93b5b225..11a014de 100755 --- a/scripts/package_sort.py +++ b/scripts/package_sort.py @@ -295,29 +295,25 @@ def build_dependency_graph(graph, root_node, spec=spec)) rtup = (req_pkg, v) graph.add_edge(rtup, ptup) - log.debug("Need to build package " "%s %s of candidates %s", req_pkg, v, pkg_versions[req_pkg]) # Is the required package one of the sub-packages # of the packages we are building? + elif req_pkg in pkg_outputs: + # Require the parent package rather than + # the sub-package + parent_pkg = pkg_outputs[req_pkg] + v = max(find_package_version(parent_pkg, pkg_versions, + spec=spec)) + rtup = (parent_pkg, v) + graph.add_edge(rtup, ptup) + log.debug("Need to build (containing) package " + "%s %s of candidates %s", + parent_pkg, v, pkg_versions[parent_pkg]) else: - if req_pkg in pkg_outputs: - # Require the parent package rather than - # the sub-package - parent_pkg = pkg_outputs[req_pkg] - v = max(find_package_version(parent_pkg, - pkg_versions, - spec=spec)) - rtup = (parent_pkg, v) - graph.add_edge(rtup, ptup) - - log.debug("Need to build (containing) package " - "%s %s of candidates %s", - parent_pkg, v, pkg_versions[parent_pkg]) - else: - log.warning("Can't find required package %s", - req_pkg) + log.warning("Can't find required package %s", req_pkg) + graph.add_edge(ptup, root_node) else: log.debug("%s has no requirements", ptup) graph.add_edge(ptup, root_node) From cfaa6a830015d43554ac1955720841decff610ec Mon Sep 17 00:00:00 2001 From: "David K. Jackson" Date: Thu, 5 Sep 2019 22:26:38 +0000 Subject: [PATCH 116/119] patch gatk python script to ensure java in conda enviroment is used --- recipes/gatk/4.1.3.0/build.sh | 1 - recipes/gatk/4.1.3.0/gatk.patch | 17 +++++++++++++++++ recipes/gatk/4.1.3.0/meta.yaml | 4 +++- 3 files changed, 20 insertions(+), 2 deletions(-) create mode 100644 recipes/gatk/4.1.3.0/gatk.patch diff --git a/recipes/gatk/4.1.3.0/build.sh b/recipes/gatk/4.1.3.0/build.sh index b95492cc..239b2b9f 100755 --- a/recipes/gatk/4.1.3.0/build.sh +++ b/recipes/gatk/4.1.3.0/build.sh @@ -6,7 +6,6 @@ PACKAGE_HOME=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM mkdir -p $PREFIX/bin mkdir -p $PACKAGE_HOME -sed -i.bak 's#!/usr/bin/env python#!/opt/anaconda1anaconda2anaconda3/bin/python#' gatk chmod +x gatk cp gatk ${PACKAGE_HOME}/gatk cp gatk-*-local.jar $PACKAGE_HOME diff --git a/recipes/gatk/4.1.3.0/gatk.patch b/recipes/gatk/4.1.3.0/gatk.patch new file mode 100644 index 00000000..db09f05e --- /dev/null +++ b/recipes/gatk/4.1.3.0/gatk.patch @@ -0,0 +1,17 @@ +--- gatk 2019-09-05 21:45:39.314033509 +0000 ++++ gatk-hacked 2019-09-05 21:51:26.357379310 +0000 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/opt/anaconda1anaconda2anaconda3/bin/python + # + # Launcher script for GATK tools. Delegates to java -jar, spark-submit, or gcloud as appropriate, + # and sets many important Spark and htsjdk properties before launch. +@@ -205,7 +205,7 @@ + + + def formatLocalJarCommand(localJar): +- return ["java"] + PACKAGED_LOCAL_JAR_OPTIONS + [ "-jar", localJar] ++ return [os.path.dirname(os.path.dirname(script)) + "/bin/java"] + PACKAGED_LOCAL_JAR_OPTIONS + [ "-jar", localJar] + + def getGatkWrapperScript(throwIfNotFound=True): + if not os.path.exists(GATK_RUN_SCRIPT): diff --git a/recipes/gatk/4.1.3.0/meta.yaml b/recipes/gatk/4.1.3.0/meta.yaml index 52aa7ead..12fdef2c 100644 --- a/recipes/gatk/4.1.3.0/meta.yaml +++ b/recipes/gatk/4.1.3.0/meta.yaml @@ -11,11 +11,13 @@ about: summary: "Genome Analysis Toolkit (GATK4)" build: - number: 0 + number: 1 source: url: https://github.com/broadinstitute/gatk/releases/download/{{ version }}/gatk-{{ version }}.zip sha256: {{ sha256 }} + patches: + - gatk.patch requirements: run: From a8622a5e4d452f78e8077e126a09de3da3130c75 Mon Sep 17 00:00:00 2001 From: "David K. Jackson" Date: Fri, 6 Sep 2019 13:28:39 +0000 Subject: [PATCH 117/119] add comment test noted that the gatk script has been patched --- recipes/gatk/4.1.3.0/gatk.patch | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/gatk/4.1.3.0/gatk.patch b/recipes/gatk/4.1.3.0/gatk.patch index db09f05e..256aa854 100644 --- a/recipes/gatk/4.1.3.0/gatk.patch +++ b/recipes/gatk/4.1.3.0/gatk.patch @@ -1,12 +1,15 @@ --- gatk 2019-09-05 21:45:39.314033509 +0000 -+++ gatk-hacked 2019-09-05 21:51:26.357379310 +0000 -@@ -1,4 +1,4 @@ ++++ gatk-hacked 2019-09-06 13:26:23.299041927 +0000 +@@ -1,4 +1,7 @@ -#!/usr/bin/env python +#!/opt/anaconda1anaconda2anaconda3/bin/python ++# ++# WARNING! This is not the standard "gatk" Python script it has been altered to use a java ++# executable from the expected install location given a conda install of gatk. # # Launcher script for GATK tools. Delegates to java -jar, spark-submit, or gcloud as appropriate, # and sets many important Spark and htsjdk properties before launch. -@@ -205,7 +205,7 @@ +@@ -205,7 +208,7 @@ def formatLocalJarCommand(localJar): From c7dc727ab90016eb33539dc00c2611f3665fe216 Mon Sep 17 00:00:00 2001 From: "David K. Jackson" Date: Fri, 6 Sep 2019 13:52:28 +0000 Subject: [PATCH 118/119] pin bam_stats/1.13.0 to htslib 1.9 --- recipes/bam_stats/1.13.0/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/bam_stats/1.13.0/meta.yaml b/recipes/bam_stats/1.13.0/meta.yaml index ac5281a4..00621e13 100644 --- a/recipes/bam_stats/1.13.0/meta.yaml +++ b/recipes/bam_stats/1.13.0/meta.yaml @@ -1,4 +1,5 @@ {% set version = "1.13.0" %} +{% set htslib_version = "1.9" %} package: name: bam_stats @@ -10,7 +11,7 @@ about: summary: "Legacy, see cancerit/PCAP-core: NGS reference implementations and helper code for the IGCG/TCGA Pan-Cancer Analysis Project." build: - number: 1 + number: 2 source: git_url: https://github.com/ICGC-TCGA-PanCancer/PCAP-core.git @@ -23,9 +24,9 @@ requirements: - {{ compiler("c") }} - make host: - - libhts-dev + - libhts-dev =={{ htslib_version }} run: - - libhts + - libhts =={{ htslib_version }} test: commands: From 0e3586f3ed7bab94fbc4ad270e7b037ca440c9d0 Mon Sep 17 00:00:00 2001 From: "David K. Jackson" Date: Sun, 8 Sep 2019 16:15:26 +0000 Subject: [PATCH 119/119] wr/0.19.0 --- recipes/wr/0.19.0/build.sh | 12 ++++++++++++ recipes/wr/0.19.0/meta.yaml | 24 ++++++++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 recipes/wr/0.19.0/build.sh create mode 100644 recipes/wr/0.19.0/meta.yaml diff --git a/recipes/wr/0.19.0/build.sh b/recipes/wr/0.19.0/build.sh new file mode 100644 index 00000000..f093a2c3 --- /dev/null +++ b/recipes/wr/0.19.0/build.sh @@ -0,0 +1,12 @@ +#!/bin/sh + +set -e + +mkdir -p "$PREFIX/bin" +cp wr "$PREFIX/bin/" + +mkdir -p "$PREFIX/etc" +cp wr_config.yml "$PREFIX/etc/" + +mkdir -p "$PREFIX/share/doc/wr" +cp README.md "$PREFIX/share/doc/wr/" diff --git a/recipes/wr/0.19.0/meta.yaml b/recipes/wr/0.19.0/meta.yaml new file mode 100644 index 00000000..bbb3df5e --- /dev/null +++ b/recipes/wr/0.19.0/meta.yaml @@ -0,0 +1,24 @@ +{% set version = "0.19.0" %} +{% set sha256 = "f139c4ec5c5e5a735608236120ec891d4070d092b88f58d21f8fb49693b6dfa1" %} + +package: + name: wr + version: "{{ version }}" + +about: + home: https://github.com/VertebrateResequencing/wr + license: GPLv3 + summary: "High performance Workflow Runner." + +build: + number: 0 + binary_relocation: false + +source: + url: https://github.com/VertebrateResequencing/wr/releases/download/v{{ version }}/wr-linux-x86-64.zip + fn: wr-{{ version }}.zip + sha256: {{ sha256 }} + +test: + commands: + - wr -h