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45 lines
1.1 KiB
Bash
45 lines
1.1 KiB
Bash
pkgname=seqlib
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pkgver=1.2.0
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pkgrel=1
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pkgdesc="C++ htslib/bwa-mem/fermi interface for interrogating sequence data"
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arch=('i686' 'x86_64')
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url="https://github.com/walaj/SeqLib"
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license=('Apache')
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depends=('htslib')
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# Do NOT add 'bwa' to depends, this package uses a flavored version of bwa.
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makedepends=('autoconf' 'git')
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source=("${pkgname}::git+https://github.com/walaj/SeqLib.git#tag=${pkgver}"
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"fermi-lite::git+https://github.com/walaj/fermi-lite.git"
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)
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prepare(){
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cd $srcdir/${pkgname}
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git submodule update --init --recursive
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sed -i '33c extern const uint8_t rle_auxtab[8];' bwa/rle.h fermi-lite/rle.h
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}
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build() {
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cd ${pkgname}
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./configure LDFLAGS='-lcurl -lcrypto' CFLAGS='-fPIC' CXXFLAGS='-fPIC'
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make
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make seqtools
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}
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package() {
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cd ${pkgname}
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make install
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install -d ${pkgdir}/usr
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mv bin lib ${pkgdir}/usr
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cd ${pkgdir}/usr/lib
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# {bwa,fml,hts,seqlib};
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for mylib in {seqlib,};
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do
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ar -x lib${mylib}.a
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gcc -shared *.o -o lib${mylib}.so
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rm -rf *.o
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done
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mkdir -p ${pkgdir}/usr/include/
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cp -rf SeqLib ${pkgdir}/usr/include/
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}
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sha256sums=('SKIP'
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'SKIP')
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