diff options
| -rw-r--r-- | .SRCINFO | 29 | ||||
| -rw-r--r-- | PKGBUILD | 60 | ||||
| -rw-r--r-- | transabyss-profile.sh | 1 | ||||
| -rw-r--r-- | transabyss.install | 35 |
4 files changed, 125 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO new file mode 100644 index 000000000000..c0ab45ab9e82 --- /dev/null +++ b/.SRCINFO @@ -0,0 +1,29 @@ +pkgbase = transabyss + pkgdesc = de novo assembly of RNA-Seq data using ABySS + pkgver = 1.5.3 + pkgrel = 1 + url = http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss + install = transabyss.install + arch = any + license = custom + depends = abyss + depends = blat + depends = bowtie2 + depends = gawk + depends = gmap-gsnap + depends = python2-biopython + depends = python2-igraph + depends = python2-pysam + depends = samtools + backup = etc/transabyss/job_script.cfg + backup = etc/transabyss/model_matcher.cfg + backup = etc/transabyss/transcriptome.cfg + source = transabyss-1.5.3.zip::https://github.com/bcgsc/transabyss/archive/1.5.3.zip + source = transabyss.install + source = transabyss-profile.sh + md5sums = 8323e601face2f5b65f2ff667ae5853e + md5sums = 9c5d33c3294e31dedada51553fa91dee + md5sums = 8367c572ac97d29bfee8b2920cfb957b + +pkgname = transabyss + diff --git a/PKGBUILD b/PKGBUILD new file mode 100644 index 000000000000..cfe3d2be1b27 --- /dev/null +++ b/PKGBUILD @@ -0,0 +1,60 @@ +# Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com> + +pkgname=transabyss +pkgver=1.5.3 +pkgrel=1 +pkgdesc='de novo assembly of RNA-Seq data using ABySS' +arch=('any') +url="http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss" +license=('custom') +depends=('abyss' 'blat' 'bowtie2' 'gawk' 'gmap-gsnap' 'python2-biopython' 'python2-igraph' 'python2-pysam' 'samtools') +source=("$pkgname-$pkgver.zip::https://github.com/bcgsc/transabyss/archive/$pkgver.zip" + transabyss.install + transabyss-profile.sh) +install=transabyss.install +backup=('etc/transabyss/job_script.cfg' + 'etc/transabyss/model_matcher.cfg' + 'etc/transabyss/transcriptome.cfg') +md5sums=('8323e601face2f5b65f2ff667ae5853e' + '9c5d33c3294e31dedada51553fa91dee' + '8367c572ac97d29bfee8b2920cfb957b') + +prepare() { + cd $srcdir/$pkgname-$pkgver + + sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' \ + -e 's|#! /usr/bin/env python|#!/usr/bin/env python2|' \ + -i transabyss* utilities/*.py + + sed -e 's|python|python2|' \ + -i analysis/fusion.py + + sed -e 's|time python|time python2|' \ + -i transabyss-analyze + + rm -r prereqs +} + +package() { + cd $srcdir/$pkgname-$pkgver + + mkdir -p $pkgdir/usr/share/transabyss \ + $pkgdir/usr/share/licenses/transabyss \ + $pkgdir/usr/bin \ + $pkgdir/etc/transabyss + + cp -r * $pkgdir/usr/share/transabyss + + for i in transabyss transabyss-analyze transabyss-merge ; do + ln -s /usr/share/transabyss/$i $pkgdir/usr/bin/$i + done + + for i in configs/*.cfg ; do + cp $i $pkgdir/etc/transabyss/$(basename $i) + ln -sf /etc/transabyss/$(basename $i) $pkgdir/usr/share/transabyss/$i + done + + install -Dm644 $srcdir/transabyss-profile.sh $pkgdir/etc/profile.d/transabyss.sh + + ln -s /usr/share/transabyss/LICENSE.txt $pkgdir/usr/share/licenses/$pkgname/LICENSE +} diff --git a/transabyss-profile.sh b/transabyss-profile.sh new file mode 100644 index 000000000000..f41f8ac03fbd --- /dev/null +++ b/transabyss-profile.sh @@ -0,0 +1 @@ +export PYTHONPATH="/usr/share/transabyss:$PYTHONPATH" diff --git a/transabyss.install b/transabyss.install new file mode 100644 index 000000000000..d65d553051b1 --- /dev/null +++ b/transabyss.install @@ -0,0 +1,35 @@ +post_install() { cat << EOF + +Configuration +------------- + +Configuration files are saved in: + + /etc/transabyss + +You will most likely want to edit the genomes section transcriptome.cfg to point +to the location of your genomes. + +Preparing Genomes +----------------- + +The genomes are usually created by downloading a reference genome, +e.g. [hg19][1], and running gmap_build, see [gmap README][2]: + + gmap_build -g -d hg19 -D /path/to/genomes chr22.fa.gz + +[1]: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/ +[2]: http://research-pub.gene.com/gmap/src/README + +Getting Started +--------------- + +transabyss installs an /etc/profile.d/transabyss.sh script that you either need +to source right now or restart your shell session. + +EOF +} + +post_upgrade() { + post_install +} |