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59 lines
2.4 KiB
Bash
59 lines
2.4 KiB
Bash
# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
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# Contributor: Clint Valentine <valentine.clint@gmail.com>
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pkgname=freebayes
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pkgver=1.3.8
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pkgrel=6
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pkgdesc="About Bayesian haplotype-based genetic polymorphism discovery and genotyping"
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arch=('x86_64')
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url="https://github.com/freebayes/freebayes"
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license=('MIT')
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depends=('tabixpp' 'seqlib' 'vcflib')
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makedepends=('ninja' 'meson' 'git' 'cmake' 'make'
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'vcftools' 'samtools' 'parallel' 'bc' 'perl'
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)
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source=(
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"${pkgname}-${pkgver}.tar.gz::${url}/archive/refs/tags/v${pkgver}.tar.gz"
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"fastahack.zip::https://github.com/ekg/fastahack/archive/refs/tags/v1.0.0.tar.gz"
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"multichoose.zip::https://github.com/vcflib/multichoose/archive/255192edd49cfe36557f7f4f0d2d6ee1c702ffbb.zip"
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"smithwaterman.zip::https://github.com/ekg/smithwaterman/archive/2610e259611ae4cde8f03c72499d28f03f6d38a7.zip"
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)
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sha256sums=('d1c24b1d1b35277e7403cd67063557998218a105c916b01a745e7704715fce67'
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'cc1c04729b0c8ba3647cbb7e15e2b490ce701d73773f30f5892d68c36a1dceae'
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'799ce24cf3784090df39dd9552d515bda9c9e7d3f24e7712dd08565680b5c8ed'
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'0806976c46a5117c7b7a6d4e174e267f05bc652885ca72a82b91e5a87600d4f9')
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prepare() {
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mv fastahack-*/* "${pkgname}-${pkgver}"/contrib/fastahack
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mv multichoose-*/* "${pkgname}-${pkgver}"/contrib/multichoose
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mv smithwaterman-*/* "${pkgname}-${pkgver}"/contrib/smithwaterman
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cd "${pkgname}-${pkgver}"
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sed -i meson.build -e "s|dependency('libvcflib'|cc.find_library('libvcflib'|g" \
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-e "s|dependency('libseqlib'|cc.find_library('libseqlib'|g" \
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-e "s|'src',|'src', '/usr/include',|g"
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sed -i src/{*.cpp,*.h} \
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-e 's|#include "../intervaltree/IntervalTree.h"|#include <vcflib/IntervalTree.h>|g' \
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-e 's|<IntervalTree.h>|<vcflib/IntervalTree.h>|g' \
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-e 's|"join.h"|<vcflib/join.h>|g' \
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-e 's|"Variant.h"|<vcflib/Variant.h>|g'
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}
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build() {
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cd "${pkgname}-${pkgver}"
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test -d build || mkdir build
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meson setup --prefix=/usr --buildtype=release \
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-Dprefer_system_deps=true -Dstatic=false \
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--default-library=shared \
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build
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cd build
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ninja -v
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}
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package() {
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cd "${pkgname}-${pkgver}"
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install -Dm 755 build/freebayes -t $pkgdir/usr/bin/
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install -Dm 755 build/bamleftalign -t $pkgdir/usr/bin/
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install -Dm644 LICENSE -t $pkgdir/usr/share/licenses/${pkgname}/
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cd build/libfreebayes_common.a.p
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gcc -shared *.o -o libfreebayes_common.so
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install -Dm755 libfreebayes_common.so -t $pkgdir/usr/lib/
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}
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