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prepare for freebayes

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This commit is contained in:
sukanka 2022-07-11 16:17:38 +08:00
parent a1ddfbb8f3
commit f53016bc2f
4 changed files with 23 additions and 6 deletions
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8
BioArchLinux/bwa/PKGBUILD
View file

@ -1,8 +1,8 @@
# Maintainer: PumpkinCheshire <sollyonzou at gmail dot com> # Maintainer: PumpkinCheshire <sollyonzou at gmail dot com>
pkgname=bwa pkgname=bwa
pkgver=v0.7.17.r27.g3ddd7b8 pkgver=0.7.17.r47.gb56db22
pkgrel=6 pkgrel=1
pkgdesc="Burrows-Wheeler Aligner maps low-divergent sequences against a large reference genome. https://doi.org/10.1093/bioinformatics/btp324" pkgdesc="Burrows-Wheeler Aligner maps low-divergent sequences against a large reference genome. https://doi.org/10.1093/bioinformatics/btp324"
arch=('x86_64') arch=('x86_64')
url="http://bio-bwa.sourceforge.net/" url="http://bio-bwa.sourceforge.net/"
@ -13,7 +13,7 @@ source=('git+https://github.com/lh3/bwa.git')
sha256sums=('SKIP') sha256sums=('SKIP')
pkgver() { pkgver() {
git -C ${pkgname} describe --long --tags | sed 's/\([^-]*-g\)/r\1/;s/-/./g' git -C ${pkgname} describe --long --tags | sed 's/^v//;s/\([^-]*-g\)/r\1/;s/-/./g'
} }
build() { build() {
@ -24,4 +24,6 @@ build() {
package() { package() {
install -Dm755 -t "${pkgdir}/usr/bin" ${srcdir}/${pkgname}/bwa install -Dm755 -t "${pkgdir}/usr/bin" ${srcdir}/${pkgname}/bwa
install -Dm644 -t "${pkgdir}/usr/share/licenses/${pkgname}" ${pkgname}/COPYING install -Dm644 -t "${pkgdir}/usr/share/licenses/${pkgname}" ${pkgname}/COPYING
cd $srcdir/${pkgname}
install -Dm644 *.h -t "${pkgdir}/usr/include/bwa"
} }

12
BioArchLinux/vcflib/PKGBUILD
View file

@ -1,7 +1,7 @@
# Maintainer: Guoyi # Maintainer: Guoyi
pkgname=vcflib pkgname=vcflib
pkgver=1.0.3 pkgver=1.0.3
pkgrel=4 pkgrel=5
pkgdesc="C++ library and cmdline tools for parsing and manipulating VCF files doi: 10.1101/2021.05.21.445151" pkgdesc="C++ library and cmdline tools for parsing and manipulating VCF files doi: 10.1101/2021.05.21.445151"
arch=('x86_64') arch=('x86_64')
url="https://github.com/vcflib/vcflib" url="https://github.com/vcflib/vcflib"
@ -64,4 +64,14 @@ package() {
mv ${pkgdir}/usr/lib/pyvcf* ${pkgdir}/usr/lib/pyvcflib.so mv ${pkgdir}/usr/lib/pyvcf* ${pkgdir}/usr/lib/pyvcflib.so
mkdir ${pkgdir}/usr/share mkdir ${pkgdir}/usr/share
mv ${pkgdir}/usr/man ${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
# install -d ${pkgdir}/usr/include/vcflib
# mv ${pkgdir}/usr/include/{*.h,*.hpp} ${pkgdir}/usr/include/vcflib
# another packages called wfa2lib
install -Dm644 $srcdir/${pkgname}/contrib/WFA2-lib/bindings/cpp/*.hpp -t ${pkgdir}/usr/include/bindings/cpp
install -Dm644 $srcdir/${pkgname}/contrib/WFA2-lib/wavefront/*.h -t ${pkgdir}/usr/include/wavefront
install -Dm644 $srcdir/${pkgname}/contrib/WFA2-lib/utils/*.h -t ${pkgdir}/usr/include/utils
install -Dm644 $srcdir/${pkgname}/contrib/WFA2-lib/system/*.h -t ${pkgdir}/usr/include/system
install -Dm644 $srcdir/${pkgname}/contrib/WFA2-lib/alignment/*.h -t ${pkgdir}/usr/include/alignment
} }

6
prepare/freebayes/PKGBUILD
View file

@ -21,11 +21,15 @@ prepare() {
sed -i "s|dependency('libvcflib'|cc.find_library('libvcflib'|g" meson.build sed -i "s|dependency('libvcflib'|cc.find_library('libvcflib'|g" meson.build
sed -i "s|dependency('libseqlib'|cc.find_library('libseqlib'|g" meson.build sed -i "s|dependency('libseqlib'|cc.find_library('libseqlib'|g" meson.build
# sed -i "167c include_directories : [ seqlib_inc]," meson.build # sed -i "167c include_directories : [ seqlib_inc]," meson.build
# fix limits
sed -i "/#include <limits>/d" intervaltree/IntervalTree.h
sed -i "8i #include <limits>" intervaltree/IntervalTree.h
} }
build() { build() {
cd "$pkgname" cd "$pkgname"
test -d build || mkdir build test -d build || mkdir build
meson --prefix=/usr --buildtype=release build -Dprefer_system_deps=true meson --prefix=/usr --buildtype=release --includedir=/usr/include/vcflib build -Dprefer_system_deps=true
cd build cd build
ninja -v ninja -v
} }

3
prepare/seqlib/PKGBUILD
View file

@ -37,7 +37,8 @@ package() {
gcc -shared *.o -o lib${mylib}.so gcc -shared *.o -o lib${mylib}.so
rm -rf *.o rm -rf *.o
done done
cd $srcdir/${pkgname}
sed -i 's|htslib/htslib/|htslib/|g' SeqLib/*.h
mkdir -p ${pkgdir}/usr/include/ mkdir -p ${pkgdir}/usr/include/
cp -rf SeqLib ${pkgdir}/usr/include/ cp -rf SeqLib ${pkgdir}/usr/include/
} }