diff --git a/prepare/arb-bio/PKGBUILD b/prepare/arb-bio/PKGBUILD new file mode 100644 index 0000000000..8cf0201f69 --- /dev/null +++ b/prepare/arb-bio/PKGBUILD @@ -0,0 +1,44 @@ +# Maintainer: Guoyi +pkgname=arb-bio +pkgver=7.0 +pkgrel=1 +pkgdesc="C++ library and cmdline tools for parsing and manipulating VCF files doi: 10.1101/2021.05.21.445151" +arch=('x86_64') +url="http://www.arb-home.de/" +license=('UNKNOWN') +depends=('lynx' 'imake' 'time' 'libxslt' +) +makedepends=('xerces-c' 'clang' 'libtirpc' 'boost') +source=("${pkgname}-${pkgver}.tgz::http://download.arb-home.de/production/2021_09_16/arb-r18733-source.tgz" +) + +md5sums=('a491b52f74fc4ddbd0ec373311ece8a0') + +prepare(){ + mv arbsrc_* ${pkgname}-${pkgver} + cd ${srcdir}/${pkgname}-${pkgver} + cp config.makefile.template config.makefile + sed -i 's|-lCORE|-lCORE -ltirpc|g' Makefile + + # If use gcc, also fail. + # gccver=$(gcc --version | grep ^gcc | sed 's/^.* //g') + # sed "s|9.3.0|9.3.0 ${gccver}|g" -i Makefile + # sed -i 's/LOOP_VECTORIZED//g' CORE/arb_strarray.cxx + # sed -i 's|LOOP_VECTORIZED=2\[||g' MULTI_PROBE/MP_sonde.cxx +} + +build() { + cd $srcdir/${pkgname}-${pkgver} + export ARBHOME=${srcdir}/${pkgname}-${pkgver} + export PATH=$ARBHOME/bin:$PATH + export XINCLUDES="-I/usr/include -I/usr/include/tirpc" + export CC=clang + export CXX=clang++ + make + make all +} + +package() { + cd $srcdir/arbsrc_* + make install DESTDIR="$pkgdir" +}