bcftools-1.3-3

2 files changed, 15 insertions, 7 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 3ddf4e279875..1bbb79622c3d 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,18 +1,21 @@
 # Generated by mksrcinfo v8
-# Sat Mar  5 10:39:13 UTC 2016
+# Sat Mar  5 10:52:13 UTC 2016
 pkgbase = bcftools
 	pkgdesc = Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
 	pkgver = 1.3
-	pkgrel = 2
+	pkgrel = 3
 	url = http://samtools.github.io/bcftools/
 	arch = i686
 	arch = x86_64
 	license = GPL
+	depends = gsl
 	depends = htslib
 	depends = perl
 	source = https://github.com/samtools/bcftools/releases/download/1.3/bcftools-1.3.tar.bz2
+	source = https://github.com/pd3/bcftools/commit/946b7eea6d699731f72124d87b3176e0ced4d25a.patch
 	source = makefile-system-htslib.patch
 	md5sums = 17f1f7d9e4a03d64a114b43ca896899f
+	md5sums = dd48ce1ac8ef91ea409f8f235574de2e
 	md5sums = e5145d175dcd242634baf42749b838f0
 
 pkgname = bcftools
diff --git a/PKGBUILD b/PKGBUILD
index 24fec0d000e5..a7c088092ef2 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -2,15 +2,17 @@
 
 pkgname=bcftools
 pkgver=1.3
-pkgrel=2
+pkgrel=3
 pkgdesc="Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants"
 arch=('i686' 'x86_64')
 url="http://samtools.github.io/bcftools/"
 license=('GPL')
-depends=('htslib' 'perl') # 'gsl'
+depends=('gsl' 'htslib' 'perl')
 source=(https://github.com/samtools/$pkgname/releases/download/$pkgver/$pkgname-$pkgver.tar.bz2
+        https://github.com/pd3/bcftools/commit/946b7eea6d699731f72124d87b3176e0ced4d25a.patch
         makefile-system-htslib.patch)
 md5sums=('17f1f7d9e4a03d64a114b43ca896899f'
+         'dd48ce1ac8ef91ea409f8f235574de2e'
          'e5145d175dcd242634baf42749b838f0')
 
 prepare() {
@@ -21,22 +23,25 @@ prepare() {
 
   # patch Makefile to make it work with a system-provided htslib
   patch -i $srcdir/makefile-system-htslib.patch
+
+  # patch gsl >= 2 problem
+  patch -i $srcdir/946b7eea6d699731f72124d87b3176e0ced4d25a.patch
 }
 
 build() {
   cd $srcdir/$pkgname-$pkgver
 
-  make prefix=/usr plugindir=/usr/lib/$pkgname # USE_GPL=1
+  make prefix=/usr plugindir=/usr/lib/$pkgname USE_GPL=1
 }
 
 check() {
   cd $srcdir/$pkgname-$pkgver
 
-  make prefix=/usr plugindir=/usr/lib/$pkgname # USE_GPL=1 test
+  make prefix=/usr plugindir=/usr/lib/$pkgname USE_GPL=1 test
 }
 
 package() {
   cd $srcdir/$pkgname-$pkgver
 
-  make prefix=/usr plugindir=/usr/lib/$pkgname DESTDIR=$pkgdir install # USE_GPL=1
+  make prefix=/usr plugindir=/usr/lib/$pkgname USE_GPL=1 DESTDIR=$pkgdir install
 }