# Description: Splice junction mapper for RNA-Seq reads
# URL: http://ccb.jhu.edu/software/tophat/
# Maintainer: Petar Petrov, slackalaxy at gmail dot com
# Depends on: boost samtools0

name=tophat
version=2.1.2
release=1
source=(https://github.com/infphilo/tophat/archive/v2.1.2/tophat-2.1.2.tar.gz
	make_pair.patch configure.patch)

build() {
	cd $name-$version
	# https://github.com/BioArchLinux/Packages/blob/master/BioArchLinux/tophat/PKGBUILD
	patch -Np1 -i $SRC/make_pair.patch
	patch -Np0 -i $SRC/configure.patch
	
	./autogen.sh

	CPPFLAGS="$CFLAGS -std=c++14" \
	./configure --prefix=/usr \
	--libdir=/usr/lib/$name \
	--libexecdir=/usr/lib/$name
	make -j1
	make install DESTDIR=$PKG
	
	mv $PKG/usr/bin/{intervaltree,sortedcontainers} $PKG/usr/lib/$name
}