# 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 }