1 files changed, 60 insertions, 0 deletions
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..cfe3d2be1b27
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,60 @@
+# Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com>
+
+pkgname=transabyss
+pkgver=1.5.3
+pkgrel=1
+pkgdesc='de novo assembly of RNA-Seq data using ABySS'
+arch=('any')
+url="http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss"
+license=('custom')
+depends=('abyss' 'blat' 'bowtie2' 'gawk' 'gmap-gsnap' 'python2-biopython' 'python2-igraph' 'python2-pysam' 'samtools')
+source=("$pkgname-$pkgver.zip::https://github.com/bcgsc/transabyss/archive/$pkgver.zip"
+        transabyss.install
+        transabyss-profile.sh)
+install=transabyss.install
+backup=('etc/transabyss/job_script.cfg'
+        'etc/transabyss/model_matcher.cfg'
+        'etc/transabyss/transcriptome.cfg')
+md5sums=('8323e601face2f5b65f2ff667ae5853e'
+         '9c5d33c3294e31dedada51553fa91dee'
+         '8367c572ac97d29bfee8b2920cfb957b')
+
+prepare() {
+  cd $srcdir/$pkgname-$pkgver
+
+  sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' \
+      -e 's|#! /usr/bin/env python|#!/usr/bin/env python2|' \
+      -i transabyss* utilities/*.py
+
+  sed -e 's|python|python2|' \
+      -i analysis/fusion.py
+
+  sed -e 's|time python|time python2|' \
+      -i transabyss-analyze
+
+  rm -r prereqs
+}
+
+package() {
+  cd $srcdir/$pkgname-$pkgver
+
+  mkdir -p $pkgdir/usr/share/transabyss \
+           $pkgdir/usr/share/licenses/transabyss \
+           $pkgdir/usr/bin \
+           $pkgdir/etc/transabyss
+
+  cp -r * $pkgdir/usr/share/transabyss
+
+  for i in transabyss transabyss-analyze transabyss-merge ; do
+    ln -s /usr/share/transabyss/$i $pkgdir/usr/bin/$i
+  done
+
+  for i in configs/*.cfg ; do
+    cp $i $pkgdir/etc/transabyss/$(basename $i)
+    ln -sf /etc/transabyss/$(basename $i) $pkgdir/usr/share/transabyss/$i
+  done
+
+  install -Dm644 $srcdir/transabyss-profile.sh $pkgdir/etc/profile.d/transabyss.sh
+
+  ln -s /usr/share/transabyss/LICENSE.txt $pkgdir/usr/share/licenses/$pkgname/LICENSE
+}