# Description: A short read aligner of DNA sequences
# URL: https://github.com/BenLangmead/bowtie/
# Maintainer: Petar Petrov, slackalaxy at gmail dot com
# Depends on:

name=bowtie
version=1.3.1
release=2
source=(https://github.com/BenLangmead/bowtie/archive/refs/tags/v${version}.tar.gz)

build() {
	cd $name-$version
	
	sed -i "s|-O3|$CFLAGS -O3|" Makefile
	make

	install -D -m755 $name $PKG/usr/bin/$name
	executables=$( ls bowtie-* )
	for b in ${executables[@]}; do
	  install -D -m755 $b $PKG/usr/bin/$b
	done

	# Copy genomic data, scripts and more
	mkdir -p $PKG/usr/share/$name
	cp -a \
	genomes indexes reads scripts \
	$PKG/usr/share/$name

	# Let's compress the E. coli genome and indexes
	gzip $PKG/usr/share/$name/genomes/*.fna
	gzip $PKG/usr/share/$name/indexes/*.ebwt
	
	find $PKG/ -name "*README*" -delete
}