From 10c1b48978ddadee8395fb613bedaa0323343bfa Mon Sep 17 00:00:00 2001 From: mencian Date: Tue, 19 Nov 2024 18:13:09 -0600 Subject: [PATCH 1/4] Rebuild bam-readcount recipe --- recipes/bam-readcount/build.sh | 22 ++++++++-------------- recipes/bam-readcount/meta.yaml | 14 +++++++++----- 2 files changed, 17 insertions(+), 19 deletions(-) diff --git a/recipes/bam-readcount/build.sh b/recipes/bam-readcount/build.sh index e4eec512b3d21..30406d3675685 100644 --- a/recipes/bam-readcount/build.sh +++ b/recipes/bam-readcount/build.sh @@ -1,10 +1,8 @@ #!/bin/bash -ex -wget https://github.com/boostorg/boost/releases/download/boost-1.85.0/boost-1.85.0-cmake.tar.gz +wget https://github.com/boostorg/boost/releases/download/boost-1.86.0/boost-1.86.0-cmake.tar.gz -mv boost-1.85.0-cmake.tar.gz vendor/boost-1.55-bamrc.tar.gz - -mkdir -p "${PREFIX}/bin" +mv boost-1.86.0-cmake.tar.gz vendor/boost-1.55-bamrc.tar.gz # Needed for building utils dependency export INCLUDES="-I{PREFIX}/include" @@ -14,26 +12,22 @@ export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" if [[ `uname` == Darwin ]]; then export LDFLAGS="${LDFLAGS} -Wl,-rpath,${PREFIX}/lib" - export CFLAGS="${CFLAGS} -Wno-unguarded-availability -Wdeprecated-non-prototype" + export CFLAGS="${CFLAGS} -Wno-unguarded-availability -Wno-deprecated-non-prototype" export CMAKE_EXTRA="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" else export CMAKE_EXTRA="" fi -mkdir -p build -pushd build -cmake -S .. -B . -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ +cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ -DCMAKE_BUILD_TYPE=Release \ -DCMAKE_CXX_COMPILER="${CXX}" \ -DCMAKE_C_COMPILER="${CC}" \ -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ -DCMAKE_C_FLAGS="${CFLAGS}" \ -Wno-dev -Wno-deprecated --no-warn-unused-cli \ - ${CMAKE_EXTRA} + "${CMAKE_EXTRA}" -make clean -make CXX="${CXX} ${LDFLAGS}" CC="${CC}" CXXFLAGS="${CXXFLAGS}" CFLAGS="${CFLAGS}" +cmake --build build -j "${CPU_COUNT}" -v -chmod 755 bin/bam-readcount -cp -f bin/bam-readcount "${PREFIX}/bin" -popd +install -d "$PREFIX/bin" +install -v -m 0755 bin/bam-readcount "$PREFIX/bin" diff --git a/recipes/bam-readcount/meta.yaml b/recipes/bam-readcount/meta.yaml index fa49a617952da..c6d593abc94b1 100644 --- a/recipes/bam-readcount/meta.yaml +++ b/recipes/bam-readcount/meta.yaml @@ -6,11 +6,11 @@ package: version: {{ version }} source: - url: https://github.com/genome/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 8ebf84d9efee0f2d3b43f0452dbf16b27337c960e25128f6a7173119e62588b8 + git_url: https://github.com/genome/bam-readcount.git + git_rev: v{{ version }} build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('bam-readcount', max_pin="x") }} @@ -19,7 +19,7 @@ requirements: - make - cmake - {{ compiler('cxx') }} - - {{ compiler('c') }} + - libtool host: - zlib - pthread-stubs @@ -39,11 +39,15 @@ about: license_file: LICENSE summary: "bam-readcount generates metrics at single nucleotide positions." dev_url: "https://github.com/genome/bam-readcount" - doc_url: "https://github.com/genome/bam-readcount/blob/master/README.md" + doc_url: "https://github.com/genome/bam-readcount/blob/v{{ version }}/README.md" extra: additional-platforms: - linux-aarch64 + - osx-arm64 identifiers: - doi:10.21105/joss.03722 - biotools:bam-readcount + skip-lints: + - uses_vcs_url + - missing_hash From f88c7ce363c9c92d8c91d5b4eb39914b5de96619 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 19 Nov 2024 18:24:51 -0600 Subject: [PATCH 2/4] Update meta.yaml --- recipes/bam-readcount/meta.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/recipes/bam-readcount/meta.yaml b/recipes/bam-readcount/meta.yaml index c6d593abc94b1..ac123a4ba935f 100644 --- a/recipes/bam-readcount/meta.yaml +++ b/recipes/bam-readcount/meta.yaml @@ -19,12 +19,15 @@ requirements: - make - cmake - {{ compiler('cxx') }} + - {{ compiler('c') }} + - autoconf + - automake - libtool + - clangdev host: - zlib - pthread-stubs - wget - - clangdev run: - python From 81676be45d7c8c08e97f6b2a7e131f6bbe7cc0c8 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 19 Nov 2024 18:28:24 -0600 Subject: [PATCH 3/4] Update meta.yaml --- recipes/bam-readcount/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/bam-readcount/meta.yaml b/recipes/bam-readcount/meta.yaml index ac123a4ba935f..3e9228ee7a197 100644 --- a/recipes/bam-readcount/meta.yaml +++ b/recipes/bam-readcount/meta.yaml @@ -23,11 +23,11 @@ requirements: - autoconf - automake - libtool - - clangdev host: - zlib - pthread-stubs - wget + - clangdev run: - python From 70c23be2077975b6c68829e91be56b88fd3ed16a Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 19 Nov 2024 18:29:18 -0600 Subject: [PATCH 4/4] Update build.sh --- recipes/bam-readcount/build.sh | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/bam-readcount/build.sh b/recipes/bam-readcount/build.sh index 30406d3675685..73ab95776b0a5 100644 --- a/recipes/bam-readcount/build.sh +++ b/recipes/bam-readcount/build.sh @@ -4,6 +4,8 @@ wget https://github.com/boostorg/boost/releases/download/boost-1.86.0/boost-1.86 mv boost-1.86.0-cmake.tar.gz vendor/boost-1.55-bamrc.tar.gz +ln -sf $(which libtool) "${PREFIX}/bin/libtool" + # Needed for building utils dependency export INCLUDES="-I{PREFIX}/include" export LIBPATH="-L${PREFIX}/lib" @@ -30,4 +32,4 @@ cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ cmake --build build -j "${CPU_COUNT}" -v install -d "$PREFIX/bin" -install -v -m 0755 bin/bam-readcount "$PREFIX/bin" +install -v -m 0755 build/bin/bam-readcount "$PREFIX/bin"