diff options
Diffstat (limited to 'PKGBUILD')
-rw-r--r-- | PKGBUILD | 119 |
1 files changed, 47 insertions, 72 deletions
@@ -1,79 +1,54 @@ -# Maintainer: Sebastian Wilzbach < sebi at wilzbach dot me > +# Maintainer: Clint Valentine <valentine.clint@gmail.com> +# Contributer: Sebastian Wilzbach <sebi at wilzbach dot me> + pkgname=biopieces -pkgver=r2311 +pkgver=2.0 pkgrel=1 -epoch= -pkgdesc="Bioinformatic framework of tools easily used and easily created" -arch=("any") -url="http://biopieces.googlecode.com/" +pkgdesc='Bioinformatic framework of tools easily used and easily created' +arch=('any') +url='http://maasha.github.io/biopieces/' 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:]]}" -} +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' + 'perl-json-xs' + 'python2' + 'ruby-terminal-table' +) +optdepends=( + 'blast: legacy blast' + 'gnuplot' + 'blat' + 'bwa' + 'bowtie' + 'bowtie2' + 'hmmer' + 'mummer' + 'muscle' + 'velvet' +) +source=("${pkgname}"-"${pkgver}".tar.gz::https://github.com/maasha/"${pkgname}"/archive/"${pkgver}".tar.gz) +sha256sums=('484877c4a844ed1e6c70594248c44b9f19a6e7a1fd08456e28f2cc83425151e8') 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 $BP_LOG - - # source the config - source "bp_conf/bashrc" - - # permission to write on bp_test - chmod a+w "bp_test" - chmod a+w "bp_test/in" - chmod a+w "bp_test/out" - - # calling test - /bin/bash "bp_test/test_all" + cd "${srcdir}"/"${pkgname}"-"${pkgver}" - # remove unnecessary test output - rm -r -f $BP_TMP + for script in bin/*; do + if [[ "${script}" =~ README ]]; then continue; fi + install -Dm755 "${script}" "${pkgdir}"/opt/"${pkgname}"/"${pkgname}"-"$( basename "${script}" )" + done } |