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# Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com>
pkgname=proovread
pkgver=2.12
pkgrel=3
pkgdesc="large-scale high accuracy PacBio correction through iterative short read consensus"
arch=('i686' 'x86_64')
url="https://github.com/BioInf-Wuerzburg/proovread"
license=('PerlArtistic')
depends=('blasr-git' 'perl-log-log4perl' 'blast+>=2.2.24' 'samtools>=1.1' 'shrimp')
source=("$pkgname::git+https://github.com/BioInf-Wuerzburg/proovread#tag=proovread-2.12")
md5sums=('SKIP')
prepare() {
cd $srcdir/$pkgname
git submodule init
git submodule update
sed -e "s|'bwa-path' => \$RealBin.'/../util/bwa/'|'bwa-path' => ''|" \
-e "s|'shrimp-path' => \$RealBin.'/../util/shrimp-2.2.3/'|'shrimp-path' => ''|" \
-e "s|'blasr-path' => \$RealBin.'/../util/blasr-1.3.1/'|'blasr-path' => ''|" \
-i proovread.cfg
sed -e 's|my $cfg_core_file = "$RealBin/../proovread.cfg";|my $cfg_core_file = "/usr/share/proovread/proovread.cfg";|' \
-e 's|my $cfg_core_file = "../proovread.cfg";|my $cfg_core_file = "/usr/share/proovread/proovread.cfg";|' \
-i bin/bam2cns \
bin/proovread \
bin/sam2cns \
bin/test_cfg.pl
}
build() {
cd $srcdir/$pkgname/util/bwa
make
}
# check() {
# cd $srcdir/$pkgname/t
# for testfile in *.t ; do
# perl $testfile
# done
# }
package() {
cd $srcdir/$pkgname
mkdir -p $pkgdir/usr/bin \
$pkgdir/usr/lib/perl5/vendor_perl \
$pkgdir/usr/share/proovread
for file in bin/* util/SeqChunker/bin/* util/bwa/bwa-proovread ; do
install -Dm755 $file $pkgdir/usr/bin/$(basename $file .pl)
done
cp -r lib/* $pkgdir/usr/lib/perl5/vendor_perl
install -Dm644 proovread.cfg $pkgdir/usr/share/proovread/proovread.cfg
}
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