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64 lines
1.9 KiB
Bash
64 lines
1.9 KiB
Bash
# Maintainer: Guoyi
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pkgname=vcflib
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pkgver=1.0.3
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pkgrel=1
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pkgdesc="C++ library and cmdline tools for parsing and manipulating VCF files doi: 10.1101/2021.05.21.445151"
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arch=('any')
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url="https://github.com/vcflib/vcflib"
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license=('MIT')
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depends=()
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makedepends=('git' 'cmake' 'make' 'htslib'
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'pandoc'
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)
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optdepends=()
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source=("git+https://github.com/vcflib/vcflib.git"
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"git+https://github.com/smarco/WFA2-lib.git"
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"fastahack.tar.gz::https://github.com/ekg/fastahack/archive/refs/tags/v1.0.0.tar.gz"
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"git+https://github.com/ekg/filevercmp.git"
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"git+https://github.com/ekg/fsom.git"
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# "intervaltree.tar.gz::https://github.com/ekg/intervaltree/archive/refs/tags/v0.1.tar.gz"
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"git+https://github.com/ekg/intervaltree.git"
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"git+https://github.com/edawson/libVCFH.git"
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"git+https://github.com/ekg/multichoose.git"
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"git+https://github.com/ekg/smithwaterman.git"
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"simde::git+https://github.com/simd-everywhere/simde-no-tests.git"
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"https://github.com/vcflib/tabixpp/archive/refs/tags/v1.1.1.tar.gz"
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)
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md5sums=('SKIP'
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'SKIP'
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'eeb7d046978d7633fe4d07def29f48c3'
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'SKIP'
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'SKIP'
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'SKIP'
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'SKIP'
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'SKIP'
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'SKIP'
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'SKIP'
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'6441f3e3bbeb6c642edc7dea1c4cf8c3')
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prepare(){
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cd ${srcdir}
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cp -rf WFA2-lib/* ${pkgname}/contrib/WFA2-lib
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cp -rf tabixpp-1.1.1/* ${pkgname}/contrib/tabixpp
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cp -rf fastahack-1.0.0 fastahack
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for module in {fastahack,filevercmp,fsom,intervaltree,libVCFH,multichoose,smithwaterman}; do
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cp -rf ${module}/* ${pkgname}/${module}
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done
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}
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build() {
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cd $srcdir/${pkgname}
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install -d build
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cd build
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cmake .. -DCAME_INSTALL_PREFIX=/usr -DPREFIX=/usr -DHTS_HEADERS=/usr/include/htslib -DHTS_LIB=/usr/lib/libhts.so
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cmake --build .
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}
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package() {
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cd "$pkgname"/build
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make install DESTDIR="$pkgdir"
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mv ${pkgdir}/usr/local/* ${pkgdir}/usr/
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mv ${pkgdir}/usr/lib/pyvcf* ${pkgdir}/usr/lib/pyvcflib.so
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rmdir ${pkgdir}/usr/local
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}
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