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+# Maintainer: Grey Christoforo <first name @ last name .net>
+
+pkgname=cufflinks-git
+pkgver=v2.2.1.r83.gb4fa050
+pkgrel=1
+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/"
+license=('Artistic')
+depends=('boost' 'eigen3' 'python2' 'samtools' 'perl')
+source=('git+https://github.com/cole-trapnell-lab/cufflinks.git')
+md5sums=('SKIP')
+
+pkgver() {
+  cd cufflinks
+  git describe --long | sed 's/\([^-]*-g\)/r\1/;s/-/./g'
+}
+
+prepare() {
+  cd cufflinks
+
+  sed -i 's,hash\[pos\]\.hash,(hash[pos].hash),g' src/GHash.hh
+
+  
+ 
+  ./autogen.sh
+  # cufflinks uses python2 but archlinux uses python3 as default python
+  perl -i -pne '$_ =~ s/python/python2/ if $_ =~ /^#!\/usr/' src/cuffmerge
+
+  export EIGEN_CPPFLAGS="-I/usr/include/eigen3"
+  export LDFLAGS="-L/usr/lib -lboost_system"
+  ./configure --prefix=/usr
+}
+
+build() {
+  cd cufflinks
+  export EIGEN_CPPFLAGS="-I/usr/include/eigen3"
+  export LDFLAGS="-L/usr/lib -lboost_system"
+  make
+}
+
+package(){
+  cd cufflinks
+  make DESTDIR="$pkgdir/" install
+}