randomly applied some patches until this builds again because upstream is shit

2 files changed, 14 insertions, 2 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 5b72ef9df685..c61ed13a914c 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,7 +1,7 @@
 pkgbase = cufflinks
 	pkgdesc = Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples..
 	pkgver = 2.2.1
-	pkgrel = 4
+	pkgrel = 5
 	url = http://cole-trapnell-lab.github.io/projects/cufflinks/
 	arch = x86_64
 	license = Artistic
diff --git a/PKGBUILD b/PKGBUILD
index 2c1db98398a4..9a364566836a 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -2,7 +2,7 @@
 
 pkgname=cufflinks
 pkgver=2.2.1
-pkgrel=4
+pkgrel=5
 pkgdesc="Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.."
 arch=("x86_64")
 url="http://cole-trapnell-lab.github.io/projects/cufflinks/"
@@ -14,6 +14,18 @@ md5sums=('80328ff4169f2778c0728a4795da85e2')
 
 prepare() {
   cd $srcdir/$pkgname-$pkgver
+ 
+  sed -i 's,hash\[pos\]\.hash,(hash[pos].hash),g' src/GHash.hh
+  
+  curl -L https://github.com/cole-trapnell-lab/cufflinks/commit/305ee7ba4fa8e8df095d293b9e0827c6a85679a8.patch | patch -p1
+  curl -L https://github.com/cole-trapnell-lab/cufflinks/commit/6c62baa6a9f3a00b71c8fc8f7f4059a7fe49824.patch | patch -p1 
+  
+  curl -L https://github.com/cole-trapnell-lab/cufflinks/pull/87/commits/b7313fffc9d1e3dc92ce8a90b0dd5b2e16cfd68f.patch | patch -p1  
+  
+  #curl -L https://github.com/cole-trapnell-lab/cufflinks/pull/108/commits/d1fdcfd1441d1a8c3b5ecaa1b60a4ae876350061.patch | patch -p1
+  #curl -L https://github.com/cole-trapnell-lab/cufflinks/pull/108/commits/80219fc315208adb4941a20701d68c25f56db756.patch | patch -p1
+
+  curl -L https://github.com/cole-trapnell-lab/cufflinks/pull/107/commits/7aa2922ab1f4ff600bd6854cdebb4be6d3b06fa5.patch | patch -p1
   
   ./autogen.sh
   # cufflinks uses python2 but archlinux uses python3 as default python