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# Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com>
pkgname=wiggletools
pkgver=1.1
pkgrel=1
pkgdesc="basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency"
arch=('i686' 'x86_64')
url="https://github.com/Ensembl/WiggleTools"
license=('Apache')
depends=('gsl' 'python2')
makedepends=('git' 'libmariadbclient' 'libpng' 'unzip')
source=("$pkgname-$pkgver.tar.gz::https://github.com/Ensembl/WiggleTools/archive/v$pkgver.tar.gz")
md5sums=('7b7052b755415936324d7919756bd070')
prepare() {
cd $srcdir/WiggleTools-$pkgver
git archive --format=zip -9 --remote=git://genome-source.cse.ucsc.edu/kent.git beta src/userApps > userApps.zip
unzip -o -d userApps -j userApps.zip
rm userApps.zip
sed -e 's|-ltinfo||g' \
-i samtools/Makefile
# use python2
sed -e 's|python test.py|python2 test.py|' \
-i Makefile
sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' \
-i python/wiggletools/*.py
}
build() {
cd $srcdir/WiggleTools-$pkgver
pushd userApps
make fetchSource
make
popd
export KENT_SRC=$PWD/userApps/kent/src
export TABIX_SRC=$PWD/userApps/samtabix
make
}
check() {
cd $srcdir/WiggleTools-$pkgver
make test
}
package() {
cd $srcdir/WiggleTools-$pkgver
install -Dm755 bin/wiggletools $pkgdir/usr/bin/wiggletools
for pythonscript in bin/*.py ; do
install -Dm755 $pythonscript $pkgdir/usr/bin/$(basename $pythonscript .py)
done
rm $pkgdir/usr/bin/__init__
for shellscript in bin/*.sh ; do
install -Dm755 $shellscript $pkgdir/usr/bin/$(basename $shellscript .sh)
done
}
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