# Description: A reference-guided assembler for RNA-Seq experiments
# URL: http://cufflinks.cbcb.umd.edu/
# Maintainer: Petar Petrov, slackalaxy at gmail dot com
# Depends on: boost gcc5 samtools0

name=cufflinks
version=2.2.1
release=1
source=(http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/$name-$version.tar.gz
	cufflinks-2.2.1-boost-1.65-tr1-removal.patch
	cufflinks-2.2.1-gcc5-make_shared.patch
	cufflinks-2.2.1-gcc6.patch
	cufflinks-2.2.1-gcc7.patch
	cufflinks-2.2.1-format-security.patch)

build() {
	cd $name-$version
	export EIGEN_CPPFLAGS="-I/usr/include/eigen3"
	export LDFLAGS="-L/usr/lib -lboost_system"
	
	export CC=gcc-5
	export CPP=cpp-5
	export CXX=g++-5
	
	# Thanks gentoo and debian!
	patch -p1 -i $SRC/cufflinks-2.2.1-gcc5-make_shared.patch
	patch -p1 -i $SRC/cufflinks-2.2.1-gcc6.patch
	patch -p1 -i $SRC/cufflinks-2.2.1-gcc7.patch
	patch -p1 -i $SRC/cufflinks-2.2.1-format-security.patch
	patch -p1 -i $SRC/cufflinks-2.2.1-boost-1.65-tr1-removal.patch

	CFLAGS="$CFLAGS -std=c++11" \
	CXXFLAGS="$CXXFLAGS -std=c++11" \
	./configure --prefix=/usr \
	--with-boost-libdir=/usr/lib \
	--disable-optim

	make
	make install DESTDIR=$PKG
}