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freebayes: can be built now

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This commit is contained in:
sukanka 2022-07-11 18:56:07 +08:00
parent f53016bc2f
commit 4a1a638c80
1 changed files with 12 additions and 9 deletions
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21
prepare/freebayes/PKGBUILD
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@ -7,24 +7,23 @@ arch=('x86_64')
url="https://github.com/freebayes/freebayes" url="https://github.com/freebayes/freebayes"
license=('MIT') license=('MIT')
depends=('tabixpp' 'vcflib' 'vcftools' 'samtools' 'parallel' 'bc') depends=('tabixpp' 'htslib')
makedepends=('ninja' 'meson' 'git' 'cmake' 'make') makedepends=('ninja' 'meson' 'git' 'cmake' 'make'
'vcflib' 'vcftools' 'samtools' 'parallel' 'bc')
optdepends=() optdepends=()
source=(git+https://github.com/freebayes/freebayes.git#tag=v${pkgver}) source=(git+https://github.com/freebayes/freebayes.git#tag=v${pkgver}
)
noextract=() noextract=()
sha256sums=('SKIP') sha256sums=('SKIP')
prepare() { prepare() {
cd "$pkgname" cd "$pkgname"
git submodule update --init --recursive git submodule update --init --recursive
# find vcflib
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 "167c include_directories : [ seqlib_inc]," meson.build
# fix limits # fix limits
sed -i "/#include <limits>/d" intervaltree/IntervalTree.h sed -i "/#include <limits>/d" intervaltree/IntervalTree.h
sed -i "8i #include <limits>" intervaltree/IntervalTree.h sed -i "8i #include <limits>" intervaltree/IntervalTree.h
cp vcflib/tabixpp/tabix.* vcflib/src
} }
build() { build() {
cd "$pkgname" cd "$pkgname"
@ -35,6 +34,10 @@ build() {
} }
package() { package() {
cd "$pkgname-$pkgver" cd "$pkgname"
install -Dm 755 build/freebayes $pkgdir/usr/bin/freebayes install -Dm 755 build/freebayes -t $pkgdir/usr/bin/
install -Dm 755 build/bamleftalign -t $pkgdir/usr/bin/
cd build/libfreebayes_common.a.p
gcc -shared *.o -o libfreebayes_common.so
install -Dm755 libfreebayes_common.so -t $pkgdir/usr/lib/
} }