From e7f636fcf1fb5d2aa800408a960fe7f4c4066636 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Fri, 1 Nov 2024 00:57:33 +0100 Subject: [PATCH 01/18] Add Eagle2 --- recipes/eagle2/build.sh | 20 +++++++++++++++++++ recipes/eagle2/meta.yaml | 43 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 recipes/eagle2/build.sh create mode 100644 recipes/eagle2/meta.yaml diff --git a/recipes/eagle2/build.sh b/recipes/eagle2/build.sh new file mode 100644 index 0000000000000..cb2187de81f73 --- /dev/null +++ b/recipes/eagle2/build.sh @@ -0,0 +1,20 @@ +#!/bin/bash + +export COMMIT_VERS="${PKG_VERSION}" +export COMMIT_DATE="$(date -Idate -u)" + +make \ + -j 4 \ + DYN_LIBS="-lz -lpthread -lbz2 -lblas" \ + CXX="$CXX -std=c++17" \ + CXXFLAG="$CXXFLAGS ${PREFIX} -D__COMMIT_ID__='\"${COMMIT_VERS}\"' -D__COMMIT_DATE__='\"${COMMIT_DATE}\"' \ + LDFLAG="$LDFLAGS" \ + HTSLIB_INC="$PREFIX" \ + HTSLIB_LIB="-lhts" \ + BOOST_INC="/usr/include"\ + BOOST_LIB_IO="-lboost_iostreams" \ + BOOST_LIB_PO="-lboost_program_options" \ + BOOST_LIB_SE="-lboost_serialization" \ + ; +install "bin/eagle" "eagle/bin" +popd diff --git a/recipes/eagle2/meta.yaml b/recipes/eagle2/meta.yaml new file mode 100644 index 0000000000000..1414afc24cf1f --- /dev/null +++ b/recipes/eagle2/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "2.4.1" %} + +package: + name: Eagle2 + version: {{ version }} + +build: + number: 1 + +source: + url: https://github.com/poruloh/Eagle/archive/refs/tags/v{{ version }}.tar.gz + sha256: 85804bfe972186ccb66e602856d6e04044302e5c0dbf9309849b0cde981e3432 + +requirements: + build: + - make + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: + - htslib >=1.9 + - bzip2 + - zlib + - boost-cpp >=1.58 + - blas >= 0.2.19 + run: + - boost-cpp + +test: + commands: + - eagle --help + +about: + home: https://github.com/poruloh/Eagle + license: GPLv3 + summary: The Eagle software estimates haplotype phase either within a genotyped cohort or using a phased reference panel. + description: + Eagle2 is now the default phasing method used by the Sanger and Michigan imputation servers and uses a new + very fast HMM-based algorithm that improves speed and accuracy over existing methods via two key ideas; + a new data structure based on the positional Burrows-Wheeler transform and a rapid search algorithm that + explores only the most relevant paths through the HMM. Compared to the Eagle1 algorithm, Eagle2 has similar + speed but much greater accuracy at sample sizes <50,000; as such, we have made the Eagle2 algorithm the default option. + (The Eagle1 algorithm can be accessed via the --v1 flag.) Eagle v2.3+ supports phasing sequence data with or without + a reference and also supports phasing chrX. \ No newline at end of file From 373f19c939537101f5185b5a44b1d7627dfde064 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Fri, 1 Nov 2024 01:04:40 +0100 Subject: [PATCH 02/18] Fix linting --- recipes/eagle2/build.sh | 9 +++------ recipes/eagle2/conda_build_config.yaml | 5 +++++ recipes/eagle2/meta.yaml | 2 +- 3 files changed, 9 insertions(+), 7 deletions(-) create mode 100644 recipes/eagle2/conda_build_config.yaml diff --git a/recipes/eagle2/build.sh b/recipes/eagle2/build.sh index cb2187de81f73..77b0c8a1e51f5 100644 --- a/recipes/eagle2/build.sh +++ b/recipes/eagle2/build.sh @@ -1,14 +1,11 @@ #!/bin/bash - -export COMMIT_VERS="${PKG_VERSION}" -export COMMIT_DATE="$(date -Idate -u)" - make \ -j 4 \ DYN_LIBS="-lz -lpthread -lbz2 -lblas" \ CXX="$CXX -std=c++17" \ - CXXFLAG="$CXXFLAGS ${PREFIX} -D__COMMIT_ID__='\"${COMMIT_VERS}\"' -D__COMMIT_DATE__='\"${COMMIT_DATE}\"' \ + CXXFLAG="$CXXFLAGS" \ LDFLAG="$LDFLAGS" \ + PREFIX="${PREFIX}" \ HTSLIB_INC="$PREFIX" \ HTSLIB_LIB="-lhts" \ BOOST_INC="/usr/include"\ @@ -16,5 +13,5 @@ make \ BOOST_LIB_PO="-lboost_program_options" \ BOOST_LIB_SE="-lboost_serialization" \ ; -install "bin/eagle" "eagle/bin" +install popd diff --git a/recipes/eagle2/conda_build_config.yaml b/recipes/eagle2/conda_build_config.yaml new file mode 100644 index 0000000000000..41b9234361f87 --- /dev/null +++ b/recipes/eagle2/conda_build_config.yaml @@ -0,0 +1,5 @@ +# current version does not build with newer compilers +cxx_compiler_version: + - 11 # [osx] +c_compiler_version: + - 11 # [osx] diff --git a/recipes/eagle2/meta.yaml b/recipes/eagle2/meta.yaml index 1414afc24cf1f..795509853cc6e 100644 --- a/recipes/eagle2/meta.yaml +++ b/recipes/eagle2/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 1 + number: 0 source: url: https://github.com/poruloh/Eagle/archive/refs/tags/v{{ version }}.tar.gz From 56ed6d48fad90a970932f9e00cb4acad1aa5bddb Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Fri, 1 Nov 2024 01:11:45 +0100 Subject: [PATCH 03/18] Fix scripts --- recipes/eagle2/build.sh | 14 ++++++++++---- recipes/eagle2/meta.yaml | 8 +++++--- 2 files changed, 15 insertions(+), 7 deletions(-) diff --git a/recipes/eagle2/build.sh b/recipes/eagle2/build.sh index 77b0c8a1e51f5..246d03b52ff9a 100644 --- a/recipes/eagle2/build.sh +++ b/recipes/eagle2/build.sh @@ -1,5 +1,10 @@ #!/bin/bash +set -euo pipefail + +echo "Building Eagle2 version ${PKG_VERSION}" + make \ + -e \ -j 4 \ DYN_LIBS="-lz -lpthread -lbz2 -lblas" \ CXX="$CXX -std=c++17" \ @@ -8,10 +13,11 @@ make \ PREFIX="${PREFIX}" \ HTSLIB_INC="$PREFIX" \ HTSLIB_LIB="-lhts" \ - BOOST_INC="/usr/include"\ + BOOST_INC="$PREFIX/include"\ BOOST_LIB_IO="-lboost_iostreams" \ BOOST_LIB_PO="-lboost_program_options" \ - BOOST_LIB_SE="-lboost_serialization" \ - ; + BOOST_LIB_SE="-lboost_serialization" || exit 1 + +echo "Installing Eagle2..." install -popd +echo "Eagle2 installation completed successfully" diff --git a/recipes/eagle2/meta.yaml b/recipes/eagle2/meta.yaml index 795509853cc6e..90f0d3f2fc8bb 100644 --- a/recipes/eagle2/meta.yaml +++ b/recipes/eagle2/meta.yaml @@ -1,7 +1,7 @@ {% set version = "2.4.1" %} package: - name: Eagle2 + name: eagle2 version: {{ version }} build: @@ -21,9 +21,11 @@ requirements: - bzip2 - zlib - boost-cpp >=1.58 - - blas >= 0.2.19 + - blas >=0.2.19 run: - - boost-cpp + - {{ pin_compatible('htslib') }} + - {{ pin_compatible('bzip2') }} + - {{ pin_compatible('boost-cpp') }} test: commands: From b2a66a6a8df2e101edcd222de441ae4bb7db21e4 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Fri, 1 Nov 2024 01:16:43 +0100 Subject: [PATCH 04/18] Fix install --- recipes/eagle2/build.sh | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/eagle2/build.sh b/recipes/eagle2/build.sh index 246d03b52ff9a..7ce79e2827fc5 100644 --- a/recipes/eagle2/build.sh +++ b/recipes/eagle2/build.sh @@ -4,10 +4,9 @@ set -euo pipefail echo "Building Eagle2 version ${PKG_VERSION}" make \ - -e \ - -j 4 \ + -e -j ${CPU_COUNT} \ DYN_LIBS="-lz -lpthread -lbz2 -lblas" \ - CXX="$CXX -std=c++17" \ + CXX="$CXX -std=c++11" \ CXXFLAG="$CXXFLAGS" \ LDFLAG="$LDFLAGS" \ PREFIX="${PREFIX}" \ @@ -19,5 +18,6 @@ make \ BOOST_LIB_SE="-lboost_serialization" || exit 1 echo "Installing Eagle2..." -install +mkdir -p "${PREFIX}/bin" +install -m 755 bin/eagle "${PREFIX}/bin/" echo "Eagle2 installation completed successfully" From 752b1a59a96daa7d56ca97e60b269cd39ac2bb49 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Fri, 1 Nov 2024 11:59:58 +0100 Subject: [PATCH 05/18] Improve build script --- recipes/eagle2/build.sh | 6 +++--- recipes/eagle2/meta.yaml | 6 +++++- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/recipes/eagle2/build.sh b/recipes/eagle2/build.sh index 7ce79e2827fc5..4e205e7aca789 100644 --- a/recipes/eagle2/build.sh +++ b/recipes/eagle2/build.sh @@ -5,17 +5,17 @@ echo "Building Eagle2 version ${PKG_VERSION}" make \ -e -j ${CPU_COUNT} \ - DYN_LIBS="-lz -lpthread -lbz2 -lblas" \ + DYN_LIBS="-lz -lpthread -lbz2 -lopenblas -lm -msse -msse2 -fopenmp -Wall" \ CXX="$CXX -std=c++11" \ CXXFLAG="$CXXFLAGS" \ LDFLAG="$LDFLAGS" \ PREFIX="${PREFIX}" \ HTSLIB_INC="$PREFIX" \ HTSLIB_LIB="-lhts" \ - BOOST_INC="$PREFIX/include"\ + BOOST_INC="$PREFIX/include" \ BOOST_LIB_IO="-lboost_iostreams" \ BOOST_LIB_PO="-lboost_program_options" \ - BOOST_LIB_SE="-lboost_serialization" || exit 1 + BOOST_LIB_SE="-lboost_serialization" || exit 1 echo "Installing Eagle2..." mkdir -p "${PREFIX}/bin" diff --git a/recipes/eagle2/meta.yaml b/recipes/eagle2/meta.yaml index 90f0d3f2fc8bb..519c491ea822f 100644 --- a/recipes/eagle2/meta.yaml +++ b/recipes/eagle2/meta.yaml @@ -6,6 +6,8 @@ package: build: number: 0 + run_exports: + - {{ pin_subpackage('eagle2', max_pin='x.x.x') }} source: url: https://github.com/poruloh/Eagle/archive/refs/tags/v{{ version }}.tar.gz @@ -21,11 +23,13 @@ requirements: - bzip2 - zlib - boost-cpp >=1.58 - - blas >=0.2.19 + - openblas >=0.2.19 run: - {{ pin_compatible('htslib') }} - {{ pin_compatible('bzip2') }} - {{ pin_compatible('boost-cpp') }} + - {{ pin_compatible('zlib') }} + - {{ pin_compatible('openblas') }} test: commands: From a7f57a16ec41b68e4170b221cc7950dae76524f2 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Sat, 2 Nov 2024 23:06:37 +0100 Subject: [PATCH 06/18] Update files --- recipes/eagle2/0001-Use-CXX-and-flags.patch | 5 +++ recipes/eagle2/build.sh | 35 ++++++++++++--------- recipes/eagle2/conda_build_config.yaml | 5 --- recipes/eagle2/meta.yaml | 5 +-- 4 files changed, 29 insertions(+), 21 deletions(-) create mode 100644 recipes/eagle2/0001-Use-CXX-and-flags.patch delete mode 100644 recipes/eagle2/conda_build_config.yaml diff --git a/recipes/eagle2/0001-Use-CXX-and-flags.patch b/recipes/eagle2/0001-Use-CXX-and-flags.patch new file mode 100644 index 0000000000000..ffe333a43d662 --- /dev/null +++ b/recipes/eagle2/0001-Use-CXX-and-flags.patch @@ -0,0 +1,5 @@ +--- src/Makefile ++++ src/Makefile +@@ -1,99 +1,99 @@ +-O = DipTreePBWT.o Eagle.o EagleImpMiss.o EagleParams.o EaglePBWT.o FileUtils.o GenoData.o HapHedge.o MapInterpolater.o MemoryUtils.o NumericUtils.o StaticMultimap.o StringUtils.o SyncedVcfData.o Timer.o memcpy.o ++O = DipTreePBWT.o Eagle.o EagleImpMiss.o EagleParams.o EaglePBWT.o FileUtils.o GenoData.o HapHedge.o MapInterpolater.o MemoryUtils.o NumericUtils.o StaticMultimap.o StringUtils.o SyncedVcfData.o Timer.o diff --git a/recipes/eagle2/build.sh b/recipes/eagle2/build.sh index 4e205e7aca789..69faa6d9236dc 100644 --- a/recipes/eagle2/build.sh +++ b/recipes/eagle2/build.sh @@ -1,23 +1,30 @@ #!/bin/bash -set -euo pipefail + +#set -euo pipefail echo "Building Eagle2 version ${PKG_VERSION}" -make \ +cd src + +sed -i.bak '/memcpy.o/d' Makefile + +# Set up environment variables for building +export BOOST_INSTALL_DIR=$PREFIX +export HTSLIB_DIR=$PREFIX +export BLAS_DIR=$PREFIX/lib +export ZLIB_STATIC_DIR=$PREFIX + +# Run make +make CC=${CXX} \ -e -j ${CPU_COUNT} \ - DYN_LIBS="-lz -lpthread -lbz2 -lopenblas -lm -msse -msse2 -fopenmp -Wall" \ - CXX="$CXX -std=c++11" \ - CXXFLAG="$CXXFLAGS" \ - LDFLAG="$LDFLAGS" \ - PREFIX="${PREFIX}" \ - HTSLIB_INC="$PREFIX" \ - HTSLIB_LIB="-lhts" \ - BOOST_INC="$PREFIX/include" \ - BOOST_LIB_IO="-lboost_iostreams" \ - BOOST_LIB_PO="-lboost_program_options" \ - BOOST_LIB_SE="-lboost_serialization" || exit 1 + CFLAGS="$CXXFLAGS -Wno-unused-result" \ + BOOST_INSTALL_DIR=$BOOST_INSTALL_DIR \ + HTSLIB_DIR=$HTSLIB_DIR \ + BLAS_DIR=$BLAS_DIR \ + ZLIB_STATIC_DIR=$ZLIB_STATIC_DIR \ + linking=static-except-glibc echo "Installing Eagle2..." mkdir -p "${PREFIX}/bin" -install -m 755 bin/eagle "${PREFIX}/bin/" +install -m 755 eagle "${PREFIX}/bin/" echo "Eagle2 installation completed successfully" diff --git a/recipes/eagle2/conda_build_config.yaml b/recipes/eagle2/conda_build_config.yaml deleted file mode 100644 index 41b9234361f87..0000000000000 --- a/recipes/eagle2/conda_build_config.yaml +++ /dev/null @@ -1,5 +0,0 @@ -# current version does not build with newer compilers -cxx_compiler_version: - - 11 # [osx] -c_compiler_version: - - 11 # [osx] diff --git a/recipes/eagle2/meta.yaml b/recipes/eagle2/meta.yaml index 519c491ea822f..3a61d2e03dbc8 100644 --- a/recipes/eagle2/meta.yaml +++ b/recipes/eagle2/meta.yaml @@ -33,8 +33,9 @@ requirements: test: commands: - - eagle --help - + - eagle -h + - eagle --vcfRef=example/ref.bcf --vcfTarget=example/target.vcf.gz --geneticMapFile=tables/genetic_map_hg19_example.txt.gz --outPrefix=target.phased + - eagle --bfile=example/EUR_test --geneticMapFile=USE_BIM --chrom=21 --outPrefix=phased --numThreads=4 --v1fast about: home: https://github.com/poruloh/Eagle license: GPLv3 From 0477092e1b66fc0800b96648e3d75019ff0112d9 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Sun, 3 Nov 2024 00:10:34 +0100 Subject: [PATCH 07/18] Set to dynamic --- recipes/eagle2/build.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/eagle2/build.sh b/recipes/eagle2/build.sh index 69faa6d9236dc..784bc36d22a00 100644 --- a/recipes/eagle2/build.sh +++ b/recipes/eagle2/build.sh @@ -22,7 +22,8 @@ make CC=${CXX} \ HTSLIB_DIR=$HTSLIB_DIR \ BLAS_DIR=$BLAS_DIR \ ZLIB_STATIC_DIR=$ZLIB_STATIC_DIR \ - linking=static-except-glibc + LIBSTDCXX_STATIC_DIR=${PREFIX}/bin \ + linking=dynamic echo "Installing Eagle2..." mkdir -p "${PREFIX}/bin" From b2d54c1b9d0840419bca472ebaf4794a77f018a8 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Sun, 3 Nov 2024 00:28:09 +0100 Subject: [PATCH 08/18] Fix directory --- recipes/eagle2/build.sh | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/recipes/eagle2/build.sh b/recipes/eagle2/build.sh index 784bc36d22a00..b4569077be555 100644 --- a/recipes/eagle2/build.sh +++ b/recipes/eagle2/build.sh @@ -1,18 +1,18 @@ #!/bin/bash -#set -euo pipefail +set -euo pipefail echo "Building Eagle2 version ${PKG_VERSION}" -cd src +cd src || exit 1 sed -i.bak '/memcpy.o/d' Makefile # Set up environment variables for building export BOOST_INSTALL_DIR=$PREFIX -export HTSLIB_DIR=$PREFIX +export HTSLIB_DIR=$PREFIX/lib export BLAS_DIR=$PREFIX/lib -export ZLIB_STATIC_DIR=$PREFIX +export ZLIB_STATIC_DIR=$PREFIX/lib # Run make make CC=${CXX} \ @@ -22,10 +22,12 @@ make CC=${CXX} \ HTSLIB_DIR=$HTSLIB_DIR \ BLAS_DIR=$BLAS_DIR \ ZLIB_STATIC_DIR=$ZLIB_STATIC_DIR \ - LIBSTDCXX_STATIC_DIR=${PREFIX}/bin \ - linking=dynamic + LIBSTDCXX_STATIC_DIR=${PREFIX}/lib \ + linking=static echo "Installing Eagle2..." mkdir -p "${PREFIX}/bin" install -m 755 eagle "${PREFIX}/bin/" echo "Eagle2 installation completed successfully" + +cd .. || exit 1 \ No newline at end of file From eaab068b5de2e8322249900d13569fe1aea55524 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Sun, 3 Nov 2024 00:34:52 +0100 Subject: [PATCH 09/18] Fix sed command --- recipes/eagle2/build.sh | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/eagle2/build.sh b/recipes/eagle2/build.sh index b4569077be555..69214495f71dd 100644 --- a/recipes/eagle2/build.sh +++ b/recipes/eagle2/build.sh @@ -1,12 +1,12 @@ #!/bin/bash -set -euo pipefail +#set -euo pipefail echo "Building Eagle2 version ${PKG_VERSION}" cd src || exit 1 -sed -i.bak '/memcpy.o/d' Makefile +sed -i.bak 's/memcpy.o//g' Makefile # Set up environment variables for building export BOOST_INSTALL_DIR=$PREFIX @@ -23,7 +23,7 @@ make CC=${CXX} \ BLAS_DIR=$BLAS_DIR \ ZLIB_STATIC_DIR=$ZLIB_STATIC_DIR \ LIBSTDCXX_STATIC_DIR=${PREFIX}/lib \ - linking=static + linking=dynamic echo "Installing Eagle2..." mkdir -p "${PREFIX}/bin" From aa3ced8364f087cfb477f98580fbf1cdc04b1e06 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Sun, 3 Nov 2024 00:36:38 +0100 Subject: [PATCH 10/18] Set -euo --- recipes/eagle2/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/eagle2/build.sh b/recipes/eagle2/build.sh index 69214495f71dd..8aece9b67e4b8 100644 --- a/recipes/eagle2/build.sh +++ b/recipes/eagle2/build.sh @@ -1,6 +1,6 @@ #!/bin/bash -#set -euo pipefail +set -euo pipefail echo "Building Eagle2 version ${PKG_VERSION}" From 6d0c0f1ecb9eca031b537bfc5d6264db177cbd3b Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Sun, 3 Nov 2024 00:50:54 +0100 Subject: [PATCH 11/18] Update example --- recipes/eagle2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/eagle2/meta.yaml b/recipes/eagle2/meta.yaml index 3a61d2e03dbc8..ea518de44230a 100644 --- a/recipes/eagle2/meta.yaml +++ b/recipes/eagle2/meta.yaml @@ -34,8 +34,8 @@ requirements: test: commands: - eagle -h - - eagle --vcfRef=example/ref.bcf --vcfTarget=example/target.vcf.gz --geneticMapFile=tables/genetic_map_hg19_example.txt.gz --outPrefix=target.phased - - eagle --bfile=example/EUR_test --geneticMapFile=USE_BIM --chrom=21 --outPrefix=phased --numThreads=4 --v1fast + - eagle --vcfRef=Eagle-2.4.1/example/ref.bcf --vcfTarget=Eagle-2.4.1/example/target.vcf.gz --geneticMapFile=Eagle-2.4.1/tables/genetic_map_hg19_example.txt.gz --outPrefix=target.phased + - eagle --bfile=Eagle-2.4.1/example/EUR_test --geneticMapFile=USE_BIM --chrom=21 --outPrefix=phased --numThreads=4 --v1fast about: home: https://github.com/poruloh/Eagle license: GPLv3 From 158bfb45d33253e5f1e15579a00b0653a183c86b Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Sun, 3 Nov 2024 11:33:14 +0100 Subject: [PATCH 12/18] Update meta.yml --- recipes/eagle2/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/eagle2/meta.yaml b/recipes/eagle2/meta.yaml index ea518de44230a..86f0815a78f6e 100644 --- a/recipes/eagle2/meta.yaml +++ b/recipes/eagle2/meta.yaml @@ -33,12 +33,13 @@ requirements: test: commands: - - eagle -h - - eagle --vcfRef=Eagle-2.4.1/example/ref.bcf --vcfTarget=Eagle-2.4.1/example/target.vcf.gz --geneticMapFile=Eagle-2.4.1/tables/genetic_map_hg19_example.txt.gz --outPrefix=target.phased - - eagle --bfile=Eagle-2.4.1/example/EUR_test --geneticMapFile=USE_BIM --chrom=21 --outPrefix=phased --numThreads=4 --v1fast + - eagle + - ls + - eagle --vcfRef=Eagle-{{ version }}/example/ref.bcf --vcfTarget=Eagle-{{ version }}/example/target.vcf.gz --geneticMapFile=Eagle-{{ version }}/tables/genetic_map_hg19_example.txt.gz --outPrefix=target.phased + - eagle --bfile=Eagle-{{ version }}/example/EUR_test --geneticMapFile=USE_BIM --chrom=21 --outPrefix=phased --numThreads=4 --v1fast about: home: https://github.com/poruloh/Eagle - license: GPLv3 + license: GPL-3.0 summary: The Eagle software estimates haplotype phase either within a genotyped cohort or using a phased reference panel. description: Eagle2 is now the default phasing method used by the Sanger and Michigan imputation servers and uses a new From dfb0e0dac897f614471e061363a34f60a8c3d5ac Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Sun, 3 Nov 2024 11:34:07 +0100 Subject: [PATCH 13/18] Update meta.yml --- recipes/eagle2/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/eagle2/meta.yaml b/recipes/eagle2/meta.yaml index 86f0815a78f6e..2f3379c57afa8 100644 --- a/recipes/eagle2/meta.yaml +++ b/recipes/eagle2/meta.yaml @@ -33,7 +33,7 @@ requirements: test: commands: - - eagle + - eagle -h - ls - eagle --vcfRef=Eagle-{{ version }}/example/ref.bcf --vcfTarget=Eagle-{{ version }}/example/target.vcf.gz --geneticMapFile=Eagle-{{ version }}/tables/genetic_map_hg19_example.txt.gz --outPrefix=target.phased - eagle --bfile=Eagle-{{ version }}/example/EUR_test --geneticMapFile=USE_BIM --chrom=21 --outPrefix=phased --numThreads=4 --v1fast From eb2698cbeed7457d631def9e7ecdb02858114e84 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Sun, 3 Nov 2024 15:53:55 +0100 Subject: [PATCH 14/18] Update meta.yml --- recipes/eagle2/meta.yaml | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/recipes/eagle2/meta.yaml b/recipes/eagle2/meta.yaml index 2f3379c57afa8..f06a5a0464cd7 100644 --- a/recipes/eagle2/meta.yaml +++ b/recipes/eagle2/meta.yaml @@ -24,22 +24,14 @@ requirements: - zlib - boost-cpp >=1.58 - openblas >=0.2.19 - run: - - {{ pin_compatible('htslib') }} - - {{ pin_compatible('bzip2') }} - - {{ pin_compatible('boost-cpp') }} - - {{ pin_compatible('zlib') }} - - {{ pin_compatible('openblas') }} test: commands: - eagle -h - - ls - - eagle --vcfRef=Eagle-{{ version }}/example/ref.bcf --vcfTarget=Eagle-{{ version }}/example/target.vcf.gz --geneticMapFile=Eagle-{{ version }}/tables/genetic_map_hg19_example.txt.gz --outPrefix=target.phased - - eagle --bfile=Eagle-{{ version }}/example/EUR_test --geneticMapFile=USE_BIM --chrom=21 --outPrefix=phased --numThreads=4 --v1fast + about: home: https://github.com/poruloh/Eagle - license: GPL-3.0 + license: GPL-3.0-only summary: The Eagle software estimates haplotype phase either within a genotyped cohort or using a phased reference panel. description: Eagle2 is now the default phasing method used by the Sanger and Michigan imputation servers and uses a new From 4b3c09fad855f868c72f1bf953a96f9431ab24ff Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Sun, 3 Nov 2024 16:05:18 +0100 Subject: [PATCH 15/18] Update meta.yml --- recipes/eagle2/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/eagle2/meta.yaml b/recipes/eagle2/meta.yaml index f06a5a0464cd7..094171d470753 100644 --- a/recipes/eagle2/meta.yaml +++ b/recipes/eagle2/meta.yaml @@ -24,6 +24,12 @@ requirements: - zlib - boost-cpp >=1.58 - openblas >=0.2.19 + run_exports: + - {{ pin_compatible('bzip2') }} + - {{ pin_compatible('zlib') }} + - {{ pin_compatible('boost-cpp') }} + - {{ pin_compatible('openblas') }} + test: commands: @@ -31,7 +37,7 @@ test: about: home: https://github.com/poruloh/Eagle - license: GPL-3.0-only + license: GPL-3.0-or-later summary: The Eagle software estimates haplotype phase either within a genotyped cohort or using a phased reference panel. description: Eagle2 is now the default phasing method used by the Sanger and Michigan imputation servers and uses a new From d96e775a6ab3205225ecb2f31f9ddbbf1d0a2efb Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Sun, 3 Nov 2024 16:49:52 +0100 Subject: [PATCH 16/18] Update meta.yml --- recipes/eagle2/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/eagle2/meta.yaml b/recipes/eagle2/meta.yaml index 094171d470753..84092b0410a33 100644 --- a/recipes/eagle2/meta.yaml +++ b/recipes/eagle2/meta.yaml @@ -24,7 +24,7 @@ requirements: - zlib - boost-cpp >=1.58 - openblas >=0.2.19 - run_exports: + run: - {{ pin_compatible('bzip2') }} - {{ pin_compatible('zlib') }} - {{ pin_compatible('boost-cpp') }} From ffbb6c10592a1092e8ce811bb5102d0f6efcfa9f Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Sun, 3 Nov 2024 19:23:07 +0100 Subject: [PATCH 17/18] Set version compiler --- recipes/eagle2/conda_build_config.yaml | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 recipes/eagle2/conda_build_config.yaml diff --git a/recipes/eagle2/conda_build_config.yaml b/recipes/eagle2/conda_build_config.yaml new file mode 100644 index 0000000000000..9c77e5c83e390 --- /dev/null +++ b/recipes/eagle2/conda_build_config.yaml @@ -0,0 +1,7 @@ +# current version does not build with newer compilers +cxx_compiler_version: + - 14 # [linux] + - 14 # [osx] +c_compiler_version: + - 14 # [linux] + - 14 # [osx] From 09d55a99c003b3e0ef2c13dec931f70b5b4b7b57 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Sun, 3 Nov 2024 20:14:12 +0100 Subject: [PATCH 18/18] Update C++ version --- recipes/eagle2/build.sh | 2 +- recipes/eagle2/conda_build_config.yaml | 7 ------- 2 files changed, 1 insertion(+), 8 deletions(-) delete mode 100644 recipes/eagle2/conda_build_config.yaml diff --git a/recipes/eagle2/build.sh b/recipes/eagle2/build.sh index 8aece9b67e4b8..73c8f41b3773f 100644 --- a/recipes/eagle2/build.sh +++ b/recipes/eagle2/build.sh @@ -17,7 +17,7 @@ export ZLIB_STATIC_DIR=$PREFIX/lib # Run make make CC=${CXX} \ -e -j ${CPU_COUNT} \ - CFLAGS="$CXXFLAGS -Wno-unused-result" \ + CFLAGS="$CXXFLAGS -Wno-unused-result -std=c++11" \ BOOST_INSTALL_DIR=$BOOST_INSTALL_DIR \ HTSLIB_DIR=$HTSLIB_DIR \ BLAS_DIR=$BLAS_DIR \ diff --git a/recipes/eagle2/conda_build_config.yaml b/recipes/eagle2/conda_build_config.yaml deleted file mode 100644 index 9c77e5c83e390..0000000000000 --- a/recipes/eagle2/conda_build_config.yaml +++ /dev/null @@ -1,7 +0,0 @@ -# current version does not build with newer compilers -cxx_compiler_version: - - 14 # [linux] - - 14 # [osx] -c_compiler_version: - - 14 # [linux] - - 14 # [osx]