wiggletools-1.1-1

1 files changed, 22 insertions, 10 deletions

diff --git a/PKGBUILD b/PKGBUILD
index d91e60c2b8ea..fe935a0de070 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,31 +1,33 @@
 # Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com>
 
 pkgname=wiggletools
-pkgver=1.0
+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 openssl)
-makedepends=(git libmariadbclient libpng unzip)
-checkdepends=(python2)
+depends=('gsl' 'python2')
+makedepends=('git' 'libmariadbclient' 'libpng' 'unzip')
 source=("$pkgname-$pkgver.tar.gz::https://github.com/Ensembl/WiggleTools/archive/v$pkgver.tar.gz")
-md5sums=('151aa1ccfaacd77183bf2ac053ee18a0')
+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 -d userApps -j userApps.zip
+  unzip -o -d userApps -j userApps.zip
   rm userApps.zip
 
-  sed -e 's|python|python2|' \
+  sed -e 's|-ltinfo||g' \
+      -i samtools/Makefile
+
+  # use python2
+  sed -e 's|python test.py|python2 test.py|' \
       -i Makefile
 
-  sed -e 's|-lgsl|-lgsl -lgslcblas|g' \
-      -e 's|-static||g' \
-      -i src/Makefile
+  sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' \
+      -i python/wiggletools/*.py
 }
 
 build() {
@@ -52,4 +54,14 @@ 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
 }