diff --git a/prepare/freebayes/PKGBUILD b/prepare/freebayes/PKGBUILD index 9ddfdaf90d..d8a6571fb8 100644 --- a/prepare/freebayes/PKGBUILD +++ b/prepare/freebayes/PKGBUILD @@ -18,7 +18,9 @@ prepare() { cd "$pkgname" git submodule update --init --recursive # find vcflib - sed -i "s|dependency('libvcflib'|cc.find_library('libvcflib'" CMakeLists.txt + sed -i "s|dependency('libvcflib'|cc.find_library('libvcflib'|g" meson.build + sed -i "s|dependency('libseqlib'|cc.find_library('libseqlib'|g" meson.build + # sed -i "167c include_directories : [ seqlib_inc]," meson.build } build() { cd "$pkgname" diff --git a/prepare/seqlib/PKGBUILD b/prepare/seqlib/PKGBUILD new file mode 100644 index 0000000000..1ccc69b10d --- /dev/null +++ b/prepare/seqlib/PKGBUILD @@ -0,0 +1,45 @@ +pkgname=seqlib +pkgver=1.2.0 +pkgrel=1 +pkgdesc="C++ htslib/bwa-mem/fermi interface for interrogating sequence data" +arch=('i686' 'x86_64') +url="https://github.com/walaj/SeqLib" +license=('Apache') +depends=('htslib') +# Do NOT add 'bwa' to depends, this package uses a flavored version of bwa. +makedepends=('autoconf' 'git') +source=("${pkgname}::git+https://github.com/walaj/SeqLib.git#tag=${pkgver}" +"fermi-lite::git+https://github.com/walaj/fermi-lite.git" +) + +prepare(){ + cd $srcdir/${pkgname} + git submodule update --init --recursive + sed -i '33c extern const uint8_t rle_auxtab[8];' bwa/rle.h fermi-lite/rle.h +} +build() { + cd ${pkgname} + ./configure LDFLAGS='-lcurl -lcrypto' CFLAGS='-fPIC' CXXFLAGS='-fPIC' + make + make seqtools +} + +package() { + cd ${pkgname} + make install + install -d ${pkgdir}/usr + mv bin lib ${pkgdir}/usr + cd ${pkgdir}/usr/lib + # {bwa,fml,hts,seqlib}; + for mylib in {seqlib,}; + do + ar -x lib${mylib}.a + gcc -shared *.o -o lib${mylib}.so + rm -rf *.o + done + + mkdir -p ${pkgdir}/usr/include/ + cp -rf SeqLib ${pkgdir}/usr/include/ +} +sha256sums=('SKIP' + 'SKIP')