From 5540b7c4393367dc46a2e0b5b7fb7e754256d729 Mon Sep 17 00:00:00 2001 From: David Lecomber Date: Wed, 27 Nov 2024 11:55:21 +0000 Subject: [PATCH 1/3] Bump build number, will this bump a rebuild on linux-aarch64? --- recipes/strelka/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/strelka/meta.yaml b/recipes/strelka/meta.yaml index 18ca2d5192d56..91fc868300062 100644 --- a/recipes/strelka/meta.yaml +++ b/recipes/strelka/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 1 + number: 2 skip: true # [osx] requirements: From b454697fcdca722a6a915b61841072ec9d39ad10 Mon Sep 17 00:00:00 2001 From: David Lecomber Date: Tue, 3 Dec 2024 17:51:22 +0000 Subject: [PATCH 2/3] update legacy builds for samtools to support linux-aarch64 and osx-arm64 --- recipes/samtools/0.1.18/build.sh | 4 ++-- recipes/samtools/0.1.18/meta.yaml | 9 ++++++++- recipes/samtools/0.1.19/build.sh | 2 +- recipes/samtools/0.1.19/meta.yaml | 10 ++++++++-- 4 files changed, 19 insertions(+), 6 deletions(-) diff --git a/recipes/samtools/0.1.18/build.sh b/recipes/samtools/0.1.18/build.sh index dc133c42d55c1..963d561450081 100644 --- a/recipes/samtools/0.1.18/build.sh +++ b/recipes/samtools/0.1.18/build.sh @@ -3,6 +3,6 @@ # does not affect the linux build # this is has been fixed in newer versions: https://github.com/samtools/samtools/issues/22 sed -i.bak -E 's/(inline void __ks_insertsort_)/static \1/g' ksort.h -make INCLUDES="-I. -I$PREFIX/include -I$PREFIX/include/ncurses" LIBCURSES="-L$PREFIX/lib -lncurses -ltinfo" LIBPATH="-L$PREFIX/lib" CC=$CC CFLAGS="-g -Wall -O2 -I$PREFIX/include -L$PREFIX/lib" +make -j ${CPU_COUNT} INCLUDES="-I. -I$PREFIX/include -I$PREFIX/include/ncurses" LIBCURSES="-L$PREFIX/lib -lncurses -ltinfo" LIBPATH="-L$PREFIX/lib" CC=$CC CFLAGS="-g -Wall -O2 -I$PREFIX/include -L$PREFIX/lib" mkdir -p $PREFIX/bin -mv samtools $PREFIX/bin \ No newline at end of file +mv samtools $PREFIX/bin diff --git a/recipes/samtools/0.1.18/meta.yaml b/recipes/samtools/0.1.18/meta.yaml index de1e934bbf01d..1e2960c3a7bd6 100644 --- a/recipes/samtools/0.1.18/meta.yaml +++ b/recipes/samtools/0.1.18/meta.yaml @@ -1,3 +1,5 @@ +{% set name = "samtools" %} + package: name: samtools version: 0.1.18 @@ -7,7 +9,9 @@ source: url: https://github.com/samtools/samtools/archive/0.1.18.tar.gz build: - number: 13 + number: 14 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: build: @@ -30,5 +34,8 @@ about: summary: Tools for dealing with SAM and BAM files extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 identifiers: - biotools:samtools diff --git a/recipes/samtools/0.1.19/build.sh b/recipes/samtools/0.1.19/build.sh index 0a00fb4756525..c27a2e240bcbb 100644 --- a/recipes/samtools/0.1.19/build.sh +++ b/recipes/samtools/0.1.19/build.sh @@ -1,5 +1,5 @@ #!/bin/sh -make INCLUDES="-I. -I$PREFIX/include -I$PREFIX/include/ncurses" LIBCURSES="-L$PREFIX/lib -lncurses -ltinfo" LIBPATH="-L$PREFIX/lib" CC=$CC CFLAGS="-g -Wall -O2 -I$PREFIX/include -L$PREFIX/lib" +make -j ${CPU_COUNT} INCLUDES="-I. -I$PREFIX/include -I$PREFIX/include/ncurses" LIBCURSES="-L$PREFIX/lib -lncurses -ltinfo" LIBPATH="-L$PREFIX/lib" CC=$CC CFLAGS="-g -Wall -O2 -I$PREFIX/include -L$PREFIX/lib" mkdir -p $PREFIX/bin mv samtools $PREFIX/bin mv bcftools/bcftools $PREFIX/bin diff --git a/recipes/samtools/0.1.19/meta.yaml b/recipes/samtools/0.1.19/meta.yaml index 65c3cab8f4be7..004471913a39d 100644 --- a/recipes/samtools/0.1.19/meta.yaml +++ b/recipes/samtools/0.1.19/meta.yaml @@ -1,3 +1,4 @@ +{% set name = "samtools" %} package: name: samtools version: 0.1.19 @@ -7,8 +8,10 @@ source: url: https://github.com/samtools/samtools/archive/refs/tags/0.1.19.tar.gz build: - number: 11 - + number: 12 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + requirements: build: - make @@ -30,5 +33,8 @@ about: summary: Tools for dealing with SAM and BAM files extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 identifiers: - biotools:samtools From cf7150d4f42ec1ad37346869f9c44e533e6a29ad Mon Sep 17 00:00:00 2001 From: David Lecomber Date: Tue, 3 Dec 2024 22:33:34 +0000 Subject: [PATCH 3/3] don't build for osx - fails with error: /opt/mambaforge/envs/bioconda/conda-bld/samtools_1733249731471/_build_env/bin/x86_64-apple-darwin13.4.0-install_name_tool: changing install names or rpaths can't be redone for: /opt/mambaforge/envs/bioconda/conda-bld/samtools_1733249731471/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/bam/misc/ace2sam (for architecture x86_64) because larger updated load commands do not fit (the program must be relinked, and you may need to use -headerpad or -headerpad_max_install_names) --- recipes/samtools/0.1.19/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/samtools/0.1.19/meta.yaml b/recipes/samtools/0.1.19/meta.yaml index 004471913a39d..4bb1df6c926f6 100644 --- a/recipes/samtools/0.1.19/meta.yaml +++ b/recipes/samtools/0.1.19/meta.yaml @@ -9,6 +9,7 @@ source: build: number: 12 + skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin="x") }}