# Maintainer: Sebastian Wilzbach < sebi at wilzbach dot me > pkgname=biopieces pkgver=r2311 pkgrel=1 epoch= pkgdesc="Bioinformatic framework of tools easily used and easily created" arch=("any") url="http://biopieces.googlecode.com/" license=('GPL2') groups=() depends=('perl' 'ruby' "perl-svg" "perl-bit-vector" "perl-term-readkey" "perl-dbi" "perl-xml-parser" "perl-carp-clan" "perl-class-inspector" "perl-html-parser" "perl-soap-lite" "perl-uri" "perl-inline" "perl-parse-recdescent" "perl-dbd-mysql" 'ruby-gnuplot' 'ruby-narray' 'perl-json-xs' 'python2' 'ruby-rubyinline' 'ruby-terminal-table') makedepends=("svn") checkdepends=() optdepends=('rubyinline' 'blast: legacy blast' 'gnuplot' 'blat' 'ray' 'bwa' 'bowtie' 'bowtie2' 'hmmer' 'mummer' 'muscle' 'velvet') provides=() conflicts=() replaces=() backup=() options=() install= changelog= source=("biopieces::svn+http://biopieces.googlecode.com/svn/trunk" "biopieces/bp_usage::svn+http://biopieces.googlecode.com/svn/wiki" "biopieces.sh") noextract=() md5sums=('SKIP' 'SKIP' '8ebebd698533ae818c8cfbef4fa8e9ca') pkgver() { cd "$srcdir/$pkgname" local ver="$(svnversion)" printf "r%s" "${ver//[[:alpha:]]}" } package() { cd "$pkgdir" mkdir -p "opt/$pkgname" cp -a "$srcdir/biopieces" "opt/" # remove svn history rm -r -f "opt/$pkgname/.svn" rm -r -f "opt/$pkgname/bp_usage/.svn" rm -r -f "opt/$pkgname/.makepkg" # patch python2 scripts find "opt/$pkgname/code_python" -type f -exec sed -i 's/#!\/usr\/bin\/python/&2/' {} \; # install exports install -Dm755 "$srcdir/$pkgname.sh" etc/profile.d/$pkgname.sh source etc/profile.d/$pkgname.sh } check() { cd "$srcdir/biopieces" # set the constant for the test suite export BP_DIR=$(pwd) export BP_TMP=$BP_DIR"/tmp" export BP_LOG="$BP_TMP/log" mkdir -p $BP_LOG # source the config source "bp_conf/bashrc" # permission to write on bp_test chmod a+w "bp_test" chmod a+w "bp_test/in" chmod a+w "bp_test/out" # calling test /bin/bash "bp_test/test_all" # remove unnecessary test output rm -r -f $BP_TMP }