Rebuild regenie recipe

recipes/regenie/build.sh

@@ -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}"

recipes/regenie/meta.yaml

@@ -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