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# Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com>
pkgname=wgs-assembler
pkgver=8.3rc2
pkgrel=1
pkgdesc="Whole-Genome Shotgun Assembler"
arch=('i686' 'x86_64')
url="http://wgs-assembler.sourceforge.net/"
license=('GPL2')
depends=('bzip2' 'gcc-libs' 'samtools')
conflicts=('blasr' 'blasr-git' 'pbdagcon' 'pbdagcon-git')
source=("http://downloads.sourceforge.net/$pkgname/wgs-$pkgver.tar.bz2")
md5sums=('70e8efea279d7061718d442a8c1217b3')
prepare() {
cd $srcdir/wgs-$pkgver
rm -rf samtools*
sed -e 's|@mkdir $(LOCAL_BIN)/TIGR|@mkdir -p $(LOCAL_BIN)/TIGR|' \
-i src/AS_RUN/Makefile
sed -e 's|-L/usr/local/lib|$(LDFLAGS)|' \
-i $(grep -rl -- -L/usr/local/lib .)
sed -e 's|KMERLIBS = libmerylguts.a libkmer.a libmeryl.a libseq.a libbio.a libutil.a|KMERLIBS = $(LOCAL_WORK)/kmer/meryl/libmerylguts.a $(LOCAL_WORK)/kmer/libkmer/libkmer.a $(LOCAL_WORK)/kmer/libmeryl/libmeryl.a $(LOCAL_WORK)/kmer/libseq/libseq.a $(LOCAL_WORK)/kmer/libbio/libbio.a $(LOCAL_WORK)/kmer/libutil/libutil.a|' \
-i src/AS_MER/Makefile
}
build() {
cd $srcdir/wgs-$pkgver/kmer
make install
cd $srcdir/wgs-$pkgver/src
make -j1
}
package() {
cd $srcdir/wgs-$pkgver
mkdir -p \
$pkgdir/usr/bin \
$pkgdir/usr/lib/java/lib \
$pkgdir/usr/share/perl5/vendor_perl
cp Linux-*/bin/* $pkgdir/usr/bin || true
cp Linux-*/lib/*.a $pkgdir/usr/lib
cp Linux-*/lib/java/*.jar $pkgdir/usr/lib/java
cp Linux-*/lib/java/lib/*.jar $pkgdir/usr/lib/java/lib
cp -r Linux-*/bin/TIGR $pkgdir/usr/share/perl5/vendor_perl
}
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