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vcflib: fix build

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This commit is contained in:
sukanka 2024-11-22 23:48:20 +08:00
parent b6626a0496
commit fdff53653d
1 changed files with 22 additions and 19 deletions
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41
BioArchLinux/vcflib/PKGBUILD
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@ -1,7 +1,7 @@
# Maintainer: Guoyi
pkgname=vcflib
pkgver=1.0.10
pkgrel=4
pkgver=1.0.12
pkgrel=1
pkgdesc="C++ library and cmdline tools for parsing and manipulating VCF files doi: 10.1101/2021.05.21.445151"
arch=('x86_64')
url="https://github.com/vcflib/vcflib"
@ -9,21 +9,21 @@ license=('MIT')
depends=('python' 'htslib' 'wfa2-lib')
makedepends=('git' 'cmake' 'pybind11' 'tabixpp' 'pandoc')
optdepends=('r: running R scripts'
'perl: running Perl scripts'
'perl: running Perl scripts'
)
source=("${pkgname}-${pkgver}.tar.gz::https://github.com/vcflib/vcflib/archive/refs/tags/v${pkgver}.tar.gz"
"fastahack.tar.gz::https://github.com/ekg/fastahack/archive/refs/tags/v1.0.0.tar.gz"
"git+https://github.com/ekg/filevercmp.git"
"git+https://github.com/ekg/fsom.git"
# "intervaltree.tar.gz::https://github.com/ekg/intervaltree/archive/refs/tags/v0.1.tar.gz"
"git+https://github.com/ekg/intervaltree.git"
"git+https://github.com/edawson/libVCFH.git"
"git+https://github.com/ekg/multichoose.git"
"git+https://github.com/ekg/smithwaterman.git"
"simde::git+https://github.com/simd-everywhere/simde-no-tests.git"
"fastahack.tar.gz::https://github.com/ekg/fastahack/archive/refs/tags/v1.0.0.tar.gz"
"git+https://github.com/ekg/filevercmp.git"
"git+https://github.com/ekg/fsom.git"
# "intervaltree.tar.gz::https://github.com/ekg/intervaltree/archive/refs/tags/v0.1.tar.gz"
"git+https://github.com/ekg/intervaltree.git"
"git+https://github.com/edawson/libVCFH.git"
"git+https://github.com/ekg/multichoose.git"
"git+https://github.com/ekg/smithwaterman.git"
"simde::git+https://github.com/simd-everywhere/simde-no-tests.git"
)
md5sums=('8851ff1b29199a8c70e6819809ea5b47'
md5sums=('5eef989c4d172d74a6f6b280ec598808'
'eeb7d046978d7633fe4d07def29f48c3'
'SKIP'
'SKIP'
@ -33,30 +33,33 @@ md5sums=('8851ff1b29199a8c70e6819809ea5b47'
'SKIP'
'SKIP')
prepare(){
prepare() {
cd ${srcdir}
cp -rf fastahack-1.0.0 fastahack
cp -rf fastahack-1.0.0 fastahack
for module in {fastahack,filevercmp,fsom,intervaltree,libVCFH,multichoose,smithwaterman}; do
cp -rf ${module}/* ${pkgname}-${pkgver}/contrib/${module}
done
cd ${pkgname}-${pkgver}
sed -i 's| contrib/tabixpp/tabix.cpp|/usr/include/tabix/tabix.cpp|g' CMakeLists.txt
sed -i 's|vcflib STATIC|vcflib SHARED|g' CMakeLists.txt
sed -i CMakeLists.txt \
-e 's| contrib/tabixpp/tabix.cpp|/usr/include/tabix/tabix.cpp|g' \
-e 's|vcflib STATIC|vcflib SHARED|g' \
-e '/install(TARGETS ${WFALIB}/d'
sed -i 's|<tabix.hpp>|<tabix/tabix.hpp>|g' src/Variant.h
}
build() {
cd $srcdir
install -d build
cmake -B build -S ${pkgname}-${pkgver} -DCMAKE_INSTALL_PREFIX=/usr -DZIG=OFF -DCMAKE_BUILD_TYPE=None -DWFA_GITMODULE=OFF \
-DCMAKE_SHARED_LINKER_FLAGS="-lwfa2cpp -lwfa2"
cmake --build build -- PREFIX=/usr HTS_HEADERS=/usr/include/htslib HTS_LIB=/usr/lib/libhts.so
cmake --build build -- PREFIX=/usr HTS_HEADERS=/usr/include/htslib HTS_LIB=/usr/lib/libhts.so
}
package() {
cd build
make install DESTDIR="$pkgdir"
mv ${pkgdir}/usr/lib/pyvcf* ${pkgdir}/usr/lib/pyvcflib.so
mv ${pkgdir}/usr/lib/pyvcf* ${pkgdir}/usr/lib/pyvcflib.so
mkdir ${pkgdir}/usr/share
mv ${pkgdir}/usr/man ${pkgdir}/usr/share
# sed -i 's|bindings/cpp/WFAligner.hpp|WFA2/bindings/cpp/WFAligner.hpp|g' ${pkgdir}/usr/include/Variant.h