diff options
| -rw-r--r-- | .SRCINFO | 50 | ||||
| -rw-r--r-- | PKGBUILD | 79 | ||||
| -rw-r--r-- | biopieces.sh | 12 |
3 files changed, 141 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO new file mode 100644 index 000000000000..dd88b994c60b --- /dev/null +++ b/.SRCINFO @@ -0,0 +1,50 @@ +pkgbase = biopieces + pkgdesc = Bioinformatic framework of tools easily used and easily created + pkgver = r2311 + pkgrel = 1 + url = http://biopieces.googlecode.com/ + arch = any + license = GPL2 + makedepends = svn + depends = perl + depends = ruby + depends = perl-svg + depends = perl-bit-vector + depends = perl-term-readkey + depends = perl-dbi + depends = perl-xml-parser + depends = perl-carp-clan + depends = perl-class-inspector + depends = perl-html-parser + depends = perl-soap-lite + depends = perl-uri + depends = perl-inline + depends = perl-parse-recdescent + depends = perl-dbd-mysql + depends = ruby-gnuplot + depends = ruby-narray + depends = perl-json-xs + depends = python2 + depends = ruby-rubyinline + depends = ruby-terminal-table + optdepends = rubyinline + optdepends = blast: legacy blast + optdepends = gnuplot + optdepends = blat + optdepends = ray + optdepends = bwa + optdepends = bowtie + optdepends = bowtie2 + optdepends = hmmer + optdepends = mummer + optdepends = muscle + optdepends = velvet + source = biopieces::svn+http://biopieces.googlecode.com/svn/trunk + source = biopieces/bp_usage::svn+http://biopieces.googlecode.com/svn/wiki + source = biopieces.sh + md5sums = SKIP + md5sums = SKIP + md5sums = 8ebebd698533ae818c8cfbef4fa8e9ca + +pkgname = biopieces + diff --git a/PKGBUILD b/PKGBUILD new file mode 100644 index 000000000000..56bcbec7a45e --- /dev/null +++ b/PKGBUILD @@ -0,0 +1,79 @@ +# 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 +} diff --git a/biopieces.sh b/biopieces.sh new file mode 100644 index 000000000000..ef41177dfced --- /dev/null +++ b/biopieces.sh @@ -0,0 +1,12 @@ +export BP_DIR="/opt/biopieces/" # Directory where biopieces are installed +export BP_DATA="~/.biopieces/data" # Contains genomic data etc. +export BP_TMP="/tmp/biopieces" # Required temporary directory. +export BP_LOG="/tmp/biopieces/log" # Required log directory. + +# create log dir +mkdir -p $BP_LOG + +if [ -f "$BP_DIR/bp_conf/bashrc" ]; then + source "$BP_DIR/bp_conf/bashrc" +fi + |