diff --git a/misc/build.sh b/misc/build.sh index 3abebd502..e93418da9 100755 --- a/misc/build.sh +++ b/misc/build.sh @@ -1,38 +1,39 @@ #! /usr/bin/env bash -export C_INCLUDE_PATH=${PREFIX}/include -export CPLUS_INCLUDE_PATH=${PREFIX}/include -export CPP_INCLUDE_PATH=${PREFIX}/include -export CXX_INCLUDE_PATH=${PREFIX}/include -export LIBRARY_PATH=${PREFIX}/lib - -# create conda PATH, if it doesn't already exist -mkdir -p $CONDA_PREFIX/bin - -# build and install ema -rm -rf ema|| true -git clone --recursive https://github.com/EdHarry/ema.git -cd ema -git checkout haplotag -git submodule update --remote -git apply ../harpy/misc/makefile.patch -git apply ../harpy/misc/remove_native.patch -make CC="$CC -fcommon" CXX="$CXX -fcommon" LDFLAGS="$LDFLAGS" -chmod +x ema -cp ema $CONDA_PREFIX/bin/ema-h -cd .. +mkdir -p PREFIX/bin +cp misc/ema-h $PREFIX/bin # Harpy executable -chmod +x harpy -cp harpy $CONDA_PREFIX/bin/ +cp harpy $PREFIX/bin/ # rules -cp rules/*.smk $CONDA_PREFIX/bin/ +cp rules/*.smk $PREFIX/bin/ # associated scripts chmod +x utilities/*.{py,R,pl} -cp utilities/*.{py,R,pl} $CONDA_PREFIX/bin/ +cp utilities/*.{py,R,pl} $PREFIX/bin/ # reports -chmod +x reports/*.Rmd -cp reports/*.Rmd $CONDA_PREFIX/bin/ \ No newline at end of file +cp reports/*.Rmd $PREFIX/bin/ + + +### deprecated? ### +#export C_INCLUDE_PATH=${PREFIX}/include +#export CPLUS_INCLUDE_PATH=${PREFIX}/include +#export CPP_INCLUDE_PATH=${PREFIX}/include +#export CXX_INCLUDE_PATH=${PREFIX}/include +#export LIBRARY_PATH=${PREFIX}/lib + +# create conda PATH, if not already existing + +# build and install ema +#rm -rf ema || true +#git clone --recursive https://github.com/EdHarry/ema.git +#cd ema && git checkout haplotag +#git submodule update --remote +#git apply ../harpy/misc/makefile.patch +#git apply ../harpy/misc/remove_native.patch +#make CC="$CC -fcommon" CXX="$CXX -fcommon" LDFLAGS="$LDFLAGS" +#chmod +x ema +#cp ema $CONDA_PREFIX/bin/ema-h +#cd .. \ No newline at end of file diff --git a/misc/meta.yaml b/misc/meta.yaml index 45335d3df..7fe229484 100644 --- a/misc/meta.yaml +++ b/misc/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.2.2" %} -{% set sha256 = "a5c3011d4caffd1e1eac96dbe8bca38f271da278ce3d0b95daf069493fef1b6a" %} +{% set version = "0.1.0" %} +{% set sha256 = "9e9dbfa11ca8be724019eecfa78ca1bb15d7c4cc01b4f0376bc03be4dc4b82d1" %} package: name: harpy @@ -14,14 +14,6 @@ build: number: 0 requirements: - build: - - git - - make - - {{ compiler('c') }} - - {{ compiler('cxx') }} - host: - - zlib - - llvm-openmp run: - bioconductor-complexheatmap - bwa