# Description: A tool for aligning sequencing reads
# URL: https://github.com/BenLangmead/bowtie2/
# Maintainer: Petar Petrov, slackalaxy at gmail dot com
# Depends on:

name=bowtie2
version=2.5.4
release=1
source=(https://github.com/BenLangmead/bowtie2/archive/v${version}/$name-$version.tar.gz)

build() {
	cd $name-$version
	
	# Use our FLAGS
	sed -i "s|-O3|$CFLAGS -O3|" Makefile
	CXXFLAGS="$CXXFLAGS" \
	make
	
	install -D -m755 $name $PKG/usr/bin/$name
	executables=$( ls bowtie2-* )
	for b in ${executables[@]}; do
	  install -D -m755 $b $PKG/usr/bin/$b
	done

	# Copy examples and scripts
	mkdir -p $PKG/usr/share/$name
	cp -a example scripts $PKG/usr/share/$name

	# Let's compress the reads and indexes
	gzip $PKG/usr/share/$name/example/reads/*.fq
	gzip $PKG/usr/share/$name/example/index/*.bt2
	
	find $PKG/ -name "*README*" -delete
}