diff --git a/recipes/odgi/build.sh b/recipes/odgi/build.sh index cd4b51ac50228..b6b6dbae4db0b 100644 --- a/recipes/odgi/build.sh +++ b/recipes/odgi/build.sh @@ -1,20 +1,26 @@ #!/bin/bash -export LIBRARY_PATH=${PREFIX}/lib -export LD_LIBRARY_PATH=${PREFIX}/lib -export CPATH=${PREFIX}/include -export C_INCLUDE_PATH=${PREFIX}/include -export CPLUS_INCLUDE_PATH=${PREFIX}/include -export CPP_INCLUDE_PATH=${PREFIX}/include -export CXX_INCLUDE_PATH=${PREFIX}/include -#cmake -H. -Bbuild -DPYTHON_EXECUTABLE:FILEPATH=$PYTHON -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-march=sandybridge -Ofast -Og' -cmake -H. -Bbuild -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-march=sandybridge -Ofast' -cmake --build build + mkdir -p $PREFIX/bin -mv bin/* $PREFIX/bin + +export INCLUDES="-I${PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" + +if [[ `uname` == "Darwin" ]]; then + export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" +else + export CONFIG_ARGS="" +fi + +cmake -S . -B build -DCMAKE_BUILD_TYPE=Generic \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" -DCMAKE_CXX_COMPILER="${CXX}" \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS}" -DEXTRA_FLAGS='-march=sandybridge -Ofast' \ + "${CONFIG_ARGS}" +cmake --build build --target install -j "${CPU_COUNT}" -v + +#mv bin/* ${PREFIX}/bin PYVER=`python -c 'import sys; print(str(sys.version_info[0])+"."+str(sys.version_info[1]))'` -mkdir -p $PREFIX/lib/python$PYVER/site-packages -cp lib/*cpython* $PREFIX/lib/python$PYVER/site-packages -cp lib/* $PREFIX/lib -#set -x -#python -c "import sys; sys.path.append('./lib'); import odgi_ffi" -#python -c "import sys; sys.path.append('./lib'); import odgi" +mkdir -p "${PREFIX}/lib/python${PYVER}/site-packages" +cp -rf lib/*cpython* "${PREFIX}/lib/python${PYVER}/site-packages" +cp -rf lib/* "${PREFIX}/lib" diff --git a/recipes/odgi/meta.yaml b/recipes/odgi/meta.yaml index 293f38ba62654..d447328cf9779 100644 --- a/recipes/odgi/meta.yaml +++ b/recipes/odgi/meta.yaml @@ -8,31 +8,29 @@ package: source: url: https://github.com/pangenome/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz sha256: 73b181c371e619b5e3e5ee87649cb8de82b054e492dcd128d93cec42be062f2f - patches: - - patch build: - skip: True # [osx or py27] + #skip: True # [osx] number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} requirements: build: - - {{ compiler('c') }} - {{ compiler('cxx') }} - - llvm-openmp # [osx] - - libgomp # [linux] - cmake - make host: + - llvm-openmp # [osx] + - libgomp # [linux] - zlib - - python - jemalloc - pybind11 run: - llvm-openmp # [osx] + - libgomp # [linux] - python + - jemalloc - pybind11 test: @@ -40,11 +38,22 @@ test: - odgi test about: - home: https://github.com/pangenome/odgi + home: "https://github.com/pangenome/odgi" license: MIT + license_family: MIT license_file: LICENSE - summary: An optimized dynamic genome/graph implementation + summary: "An optimized dynamic genome/graph implementation." + dev_url: "https://github.com/pangenome/odgi" + doc_url: "https://github.com/pangenome/odgi/blob/v{{ version }}/README.md" extra: recipe-maintainers: - AndreaGuarracino + identifiers: + - doi:10.1093/bioinformatics/btac308 + - biotools:odgi + - usegalaxy-eu:odgi_viz + - usegalaxy-eu:odgi_build + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/odgi/patch b/recipes/odgi/patch deleted file mode 100644 index f5e417a8ecd37..0000000000000 --- a/recipes/odgi/patch +++ /dev/null @@ -1,12 +0,0 @@ -diff --git a/src/pythonmodule.cpp b/src/pythonmodule.cpp -index 6a7942b..e38b12b 100644 ---- a/src/pythonmodule.cpp -+++ b/src/pythonmodule.cpp -@@ -5,6 +5,7 @@ - #include - #include - #include -+#include - - namespace py = pybind11; -