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Rebuild regenie recipe #52074

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40 changes: 20 additions & 20 deletions recipes/regenie/build.sh
Original file line number Diff line number Diff line change
@@ -3,29 +3,29 @@
set -e
set -x

if [ "$(uname)" = "Darwin" ]; then
# LDFLAGS fix: https://github.com/AnacondaRecipes/intel_repack-feedstock/issues/8
export LDFLAGS="-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib"
export INCLUDES="-I${PREFIX}/include"
export LIBPATH="-L${PREFIX}/lib"
export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"

if [[ "$(uname)" = "Darwin" ]]; then
# LDFLAGS fix: https://github.com/AnacondaRecipes/intel_repack-feedstock/issues/8
export LDFLAGS="${LDFLAGS} -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib"
export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
else
export LDFLAGS="-L$PREFIX/lib"
export MKL_THREADING_LAYER="GNU"
export LDFLAGS="${LDFLAGS} -L$PREFIX/lib"
export MKL_THREADING_LAYER="GNU"
export CONFIG_ARGS=""
fi
# https://bioconda.github.io/troubleshooting.html#zlib-errors
export CFLAGS="-I$PREFIX/include"
export CPATH=${PREFIX}/include


mkdir -p build
export CFLAGS="${CFLAGS} -O3 -I$PREFIX/include"
export CPATH="${PREFIX}/include"

cmake \
-DBUILD_SHARED_LIBS:BOOL=ON \
-DCMAKE_PREFIX_PATH:PATH=${PREFIX} \
-DCMAKE_INSTALL_PREFIX:PATH=${PREFIX} \
-DCMAKE_BUILD_TYPE="Release" \
-S "${SRC_DIR}" \
-B build

make -C build -j1 regenie
make -C build install
cmake -S . -B build -DCMAKE_BUILD_TYPE="Release" \
-DCMAKE_INSTALL_PREFIX="${PREFIX}" \
-DCMAKE_CXX_COMPILER="${CXX}" \
-DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
-DBOOST_ROOT="${PREFIX}" \
"${CONFIG_ARGS}"

# bash test/test_conda.sh --path "${SRC_DIR}"
cmake --build build --target install -j "${CPU_COUNT}"
104 changes: 0 additions & 104 deletions recipes/regenie/build_failure.osx-64.yaml

This file was deleted.

2 changes: 0 additions & 2 deletions recipes/regenie/conda_build_config.yaml

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29 changes: 8 additions & 21 deletions recipes/regenie/meta.yaml
Original file line number Diff line number Diff line change
@@ -10,25 +10,10 @@ source:
url: https://github.com/rgcgithub/regenie/archive/v{{ version }}.tar.gz
sha256: {{ sha256 }}
patches:
# Fixing postrelease issues
# - patches/0001-use-shared-cxxopts.patch
# - patches/0002-import-shared-Eigen3.patch
# - patches/0003-use-conda-cmakelists.patch
# - patches/0004-fix-fail-exit-on-help.patch
# - patches/0005-use-conda-cmakelist-file.patch
# - patches/0006-fix-cmakelist-file.patch
# - patches/0007-fix-cmakelist-file-for-osx.patch
# - patches/0008-fix-cmakelist-file-for-osx-eigen4.patch
# - patches/0009-update-cmake-file-for-conda.patch
# - patches/0010-update-cmakelist-file-for-v3.2.7.patch
# - patches/0011-update-cmakelist-file-for-v3.2.9.patch
# - patches/0012-update-cmakelist-file-for-v3.4.patch
# - patches/0013-update-cmakelist-file-for-v3.4.1.patch
# - patches/0014-update-cmakelist.txt-for-v3.5.patch
- patches/0015-update-cmakelist.txt-for-v3.6.patch

build:
number: 0
number: 1
run_exports:
- {{ pin_subpackage('regenie', max_pin="x") }}

@@ -40,9 +25,9 @@ requirements:
- binutils >=2.33.1 # [linux]
- cmake >=3.13
- make
host:
- llvm-openmp # [osx]
- libgomp # [linux]
host:
- bgenix >=1.1.7
- boost-cpp 1.74
- liblapack * *mkl
@@ -51,11 +36,11 @@ requirements:
- zlib
- zstd
run:
- llvm-openmp # [osx]
- libgomp # [linux]
- boost-cpp 1.74
- mkl >=2020.4
- sqlite
- zlib
- zstd

test:
commands:
@@ -64,15 +49,17 @@ test:
- regenie --version

about:
home: https://rgcgithub.github.io/regenie/
home: https://rgcgithub.github.io/regenie
license: MIT
license_family: MIT
license_file: LICENSE
summary: 'Regenie is a C++ program for whole genome regression modelling of large genome-wide association studies (GWAS).'
dev_url: https://github.com/rgcgithub/regenie
doc_url: https://rgcgithub.github.io/regenie/options/
doc_url: https://rgcgithub.github.io/regenie/options

extra:
recipe-maintainers:
- matuskosut
- joellembatchou
identifiers:
- doi:10.1038/s41588-021-00870-7
25 changes: 0 additions & 25 deletions recipes/regenie/patches/0001-use-shared-cxxopts.patch

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27 changes: 0 additions & 27 deletions recipes/regenie/patches/0002-import-shared-Eigen3.patch

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116 changes: 0 additions & 116 deletions recipes/regenie/patches/0003-use-conda-cmakelists.patch

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30 changes: 0 additions & 30 deletions recipes/regenie/patches/0004-fix-fail-exit-on-help.patch

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307 changes: 0 additions & 307 deletions recipes/regenie/patches/0005-use-conda-cmakelist-file.patch

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317 changes: 0 additions & 317 deletions recipes/regenie/patches/0006-fix-cmakelist-file.patch

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306 changes: 0 additions & 306 deletions recipes/regenie/patches/0007-fix-cmakelist-file-for-osx.patch

This file was deleted.

306 changes: 0 additions & 306 deletions recipes/regenie/patches/0008-fix-cmakelist-file-for-osx-eigen4.patch

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306 changes: 0 additions & 306 deletions recipes/regenie/patches/0009-update-cmake-file-for-conda.patch

This file was deleted.

306 changes: 0 additions & 306 deletions recipes/regenie/patches/0010-update-cmakelist-file-for-v3.2.7.patch

This file was deleted.

300 changes: 0 additions & 300 deletions recipes/regenie/patches/0011-update-cmakelist-file-for-v3.2.9.patch

This file was deleted.

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