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| author | BioArchLinuxBot | 2023-03-22 05:27:21 +0000 |
|---|---|---|
| committer | BioArchLinuxBot | 2023-03-22 05:27:21 +0000 |
| commit | e35e22d91f0414db0fa1e1178600b3abff3e2b59 (patch) | |
| tree | 50ffd2e4321d3cac7e6bb74a2160990d9c8ed790 | |
| parent | b99ca3b8c41c0529347be7c57b3e8ccbece96435 (diff) | |
| download | aur-e35e22d91f0414db0fa1e1178600b3abff3e2b59.tar.gz | |
[lilac] updated to 1.3.7-1
| -rw-r--r-- | .SRCINFO | 13 | ||||
| -rw-r--r-- | PKGBUILD | 39 |
2 files changed, 25 insertions, 27 deletions
@@ -1,7 +1,7 @@ pkgbase = freebayes pkgdesc = About Bayesian haplotype-based genetic polymorphism discovery and genotyping - pkgver = 1.3.6 - pkgrel = 4 + pkgver = 1.3.7 + pkgrel = 1 url = https://github.com/freebayes/freebayes arch = x86_64 license = MIT @@ -10,14 +10,15 @@ pkgbase = freebayes makedepends = git makedepends = cmake makedepends = make - makedepends = vcflib makedepends = vcftools makedepends = samtools makedepends = parallel makedepends = bc + makedepends = perl depends = tabixpp - depends = htslib - source = git+https://github.com/freebayes/freebayes.git#tag=v1.3.6 - sha256sums = SKIP + depends = seqlib + depends = vcflib + source = freebayes-1.3.7.tar.gz::https://github.com/freebayes/freebayes/archive/refs/tags/v1.3.7.tar.gz + sha256sums = 89c2202aaa82925bc6a49e04df593e5ef3b1547b3b514efcbd490a54d8ad200b pkgname = freebayes @@ -1,44 +1,41 @@ # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net> # Contributor: Clint Valentine <valentine.clint@gmail.com> pkgname=freebayes -pkgver=1.3.6 -pkgrel=4 +pkgver=1.3.7 +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' 'htslib') +depends=('tabixpp' 'seqlib' 'vcflib') makedepends=('ninja' 'meson' 'git' 'cmake' 'make' -'vcflib' 'vcftools' 'samtools' 'parallel' 'bc') -optdepends=() - -source=("git+https://github.com/freebayes/freebayes.git#tag=v${pkgver}") -noextract=() -sha256sums=('SKIP') +'vcftools' 'samtools' 'parallel' 'bc' 'perl' +) +source=("${pkgname}-${pkgver}.tar.gz::${url}/archive/refs/tags/v${pkgver}.tar.gz") +sha256sums=('89c2202aaa82925bc6a49e04df593e5ef3b1547b3b514efcbd490a54d8ad200b') prepare() { - cd "$pkgname" - git submodule update --init --recursive + cd "${pkgname}-${pkgver}" - # fix limits - sed -i "/#include <limits>/d" intervaltree/IntervalTree.h - sed -i "8i #include <limits>" intervaltree/IntervalTree.h - cp vcflib/tabixpp/tabix.* vcflib/src + 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|#include "../intervaltree/IntervalTree.h"|#include <IntervalTree.h>|g' src/{*.cpp,*.h} } build() { - cd "$pkgname" + cd "${pkgname}-${pkgver}" test -d build || mkdir build - meson --prefix=/usr --buildtype=release --includedir=/usr/include/vcflib build - #marked it because meson.build:9:0: ERROR: Unknown options: "prefer_system_deps" - #-Dprefer_system_deps=true + meson setup --prefix=/usr --buildtype=release \ + -Dprefer_system_deps=true -Dstatic=false \ + --default-library=shared \ + build cd build ninja -v } package() { - cd "$pkgname" + cd "${pkgname}-${pkgver}" install -Dm 755 build/freebayes -t $pkgdir/usr/bin/ install -Dm 755 build/bamleftalign -t $pkgdir/usr/bin/ + install -Dm644 LICENSE -t $pkgdir/usr/share/licenses/${pkgname}/ cd build/libfreebayes_common.a.p gcc -shared *.o -o libfreebayes_common.so install -Dm755 libfreebayes_common.so -t $pkgdir/usr/lib/ |