mirror of
https://github.com/BioArchLinux/Packages.git
synced 2025-03-10 12:02:42 +00:00
40 lines
1.2 KiB
Bash
40 lines
1.2 KiB
Bash
# maintainer: Guoyi
|
|
pkgname=freebayes
|
|
pkgver=1.3.6
|
|
pkgrel=1
|
|
pkgdesc="About Bayesian haplotype-based genetic polymorphism discovery and genotyping"
|
|
arch=('x86_64')
|
|
url="https://github.com/freebayes/freebayes"
|
|
license=('MIT')
|
|
|
|
depends=('tabixpp' 'vcflib' 'vcftools' 'samtools' 'parallel' 'bc')
|
|
makedepends=('ninja' 'meson' 'git' 'cmake' 'make')
|
|
optdepends=()
|
|
|
|
source=(git+https://github.com/freebayes/freebayes.git#tag=v${pkgver})
|
|
noextract=()
|
|
sha256sums=('SKIP')
|
|
prepare() {
|
|
cd "$pkgname"
|
|
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
|
|
sed -i "/#include <limits>/d" intervaltree/IntervalTree.h
|
|
sed -i "8i #include <limits>" intervaltree/IntervalTree.h
|
|
}
|
|
build() {
|
|
cd "$pkgname"
|
|
test -d build || mkdir build
|
|
meson --prefix=/usr --buildtype=release --includedir=/usr/include/vcflib build -Dprefer_system_deps=true
|
|
cd build
|
|
ninja -v
|
|
}
|
|
|
|
package() {
|
|
cd "$pkgname-$pkgver"
|
|
install -Dm 755 build/freebayes $pkgdir/usr/bin/freebayes
|
|
}
|