1 files changed, 79 insertions, 0 deletions
diff --git a/PKGBUILD b/PKGBUILD
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+# 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
+}