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# Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com>
pkgname=proovread
pkgver=2.12
pkgrel=1
pkgdesc="large-scale high accuracy PacBio correction through iterative short read consensus"
arch=('any')
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
}
build() {
cd $srcdir/$pkgname/util/bwa
make
}
package() {
cd $srcdir/$pkgname
mkdir -p $pkgdir/usr/bin \
$pkgdir/usr/lib/perl5/vendor_perl
for file in bin/* util/SeqChunker/bin/* ; do
install -Dm755 $file $pkgdir/usr/bin/$(basename $file .pl)
done
cp -r lib/* $pkgdir/usr/lib/perl5/vendor_perl
}
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