diff options
| author | Christian Krause | 2015-08-06 15:59:43 +0200 |
|---|---|---|
| committer | Christian Krause | 2015-08-06 15:59:43 +0200 |
| commit | a5379b4e9e99557986f73326273b565256b69097 (patch) | |
| tree | 4171b64975a9b4f0102d91dfe37c9db8e7f49c97 | |
| download | aur-wgs-assembler.tar.gz | |
wgs-assembler-8.3rc2-1
| -rw-r--r-- | .SRCINFO | 20 | ||||
| -rw-r--r-- | PKGBUILD | 53 |
2 files changed, 73 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO new file mode 100644 index 000000000000..05c3fdd64c71 --- /dev/null +++ b/.SRCINFO @@ -0,0 +1,20 @@ +pkgbase = wgs-assembler + pkgdesc = Whole-Genome Shotgun Assembler + pkgver = 8.3rc2 + pkgrel = 1 + url = http://wgs-assembler.sourceforge.net/ + arch = i686 + arch = x86_64 + license = GPL2 + depends = bzip2 + depends = gcc-libs + depends = samtools + conflicts = blasr + conflicts = blasr-git + conflicts = pbdagcon + conflicts = pbdagcon-git + source = http://downloads.sourceforge.net/wgs-assembler/wgs-8.3rc2.tar.bz2 + md5sums = 70e8efea279d7061718d442a8c1217b3 + +pkgname = wgs-assembler + diff --git a/PKGBUILD b/PKGBUILD new file mode 100644 index 000000000000..77fff2b8d377 --- /dev/null +++ b/PKGBUILD @@ -0,0 +1,53 @@ +# 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 +} |