This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository giira.
commit d2d6cd503604d17b990fe4dcf3fa86e5dd74dc9f Author: Andreas Tille <[email protected]> Date: Sat Feb 8 00:07:20 2014 +0100 Inject initial debian/ dir --- debian/changelog | 5 +++++ debian/compat | 1 + debian/control | 26 ++++++++++++++++++++++++++ debian/copyright | 27 +++++++++++++++++++++++++++ debian/get-orig-source | 30 ++++++++++++++++++++++++++++++ debian/rules | 11 +++++++++++ debian/source/format | 1 + debian/upstream | 9 +++++++++ debian/watch | 5 +++++ 9 files changed, 115 insertions(+) diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..4a3709e --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +giira (0.0.20131015-1) UNRELEASED; urgency=low + + * Initial release (Closes: #<bug>) + + -- Andreas Tille <[email protected]> Fri, 07 Feb 2014 11:38:38 +0100 diff --git a/debian/compat b/debian/compat new file mode 100644 index 0000000..ec63514 --- /dev/null +++ b/debian/compat @@ -0,0 +1 @@ +9 diff --git a/debian/control b/debian/control new file mode 100644 index 0000000..2d0ab4e --- /dev/null +++ b/debian/control @@ -0,0 +1,26 @@ +Source: giira +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Andreas Tille <[email protected]> +Section: science +Priority: optional +Build-Depends: debhelper (>= 9), + javahelper (>=0.25), + default-jdk +Standards-Version: 3.9.5 +Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/giira.git +Vcs-Git: git://anonscm.debian.org/debian-med/giira.git +Homepage: http://sourceforge.net/projects/giira/ +X-Python-Version: >= 2.6 + +Package: giira +Architecture: any +Depends: ${misc:Depends}, + ${java:Depends} +Description: RNA-Seq driven gene finding incorporating ambiguous reads + GIIRA is a gene prediction method that identifies potential coding + regions exclusively based on the mapping of reads from an RNA-Seq + experiment. It was foremost designed for prokaryotic gene prediction + and is able to resolve genes within the expressed region of an operon. + However, it is also applicable to eukaryotes and predicts exon intron + structures as well as alternative isoforms. + diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..8dc8476 --- /dev/null +++ b/debian/copyright @@ -0,0 +1,27 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: GIIRA +Upstream-Contact: Franziska Zickmann <[email protected]> +Source: http://sourceforge.net/projects/giira/files/ + +Files: * +Copyright: 2013 Franziska Zickmann <[email protected]> + Robert Koch-Institut +License: GPLv3 + +Files: debian/* +Copyright: 2014 Andreas Tille <[email protected]> +License: GPLv3 + +License: GPLv3 + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + . + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + . + On Debian systems you can find the full text of the GNU General Public + License version 3 at /usr/share/common-licenses/GPL-3. diff --git a/debian/get-orig-source b/debian/get-orig-source new file mode 100755 index 0000000..4c733f1 --- /dev/null +++ b/debian/get-orig-source @@ -0,0 +1,30 @@ +#!/bin/sh +# get source for giira to obtain documentation source from SVN + +set -e +# set -x +NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` +COMPRESSION=xz +VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'` + +mkdir -p ../tarballs +cd ../tarballs +TARDIR=${NAME}-${VERSION} +EXAMPLEDIR=${NAME}-example-${VERSION} + +rm -rf $TARDIR $EXAMPLEDIR +wget http://sourceforge.net/projects/${NAME}/files/GIIRA.zip +unzip GIIRA.zip +mv GIIRA $TARDIR +mkdir -p $EXAMPLEDIR +mv $TARDIR/example $EXAMPLEDIR +cd $TARDIR +rm -f *.jar +# fetch source from SVN +svn export svn://svn.code.sf.net/p/${NAME}/code/trunk/src +cd .. + +GZIP="--best --no-name" XZ_OPT="-6v" tar --owner=root --group=root --mode=a+rX -a -cf ${NAME}_${VERSION}.orig.tar.${COMPRESSION} ${TARDIR} +rm -rf ${TARDIR} +GZIP="--best --no-name" XZ_OPT="-6v" tar --owner=root --group=root --mode=a+rX -a -cf ${NAME}-example_${VERSION}.orig.tar.${COMPRESSION} ${EXAMPLEDIR} +rm -rf ${EXAMPLEDIR} diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..92a055e --- /dev/null +++ b/debian/rules @@ -0,0 +1,11 @@ +#!/usr/bin/make -f + +# DH_VERBOSE := 1 + +export JAVA_HOME=/usr/lib/jvm/default-java + +%: + dh $@ --with javahelper + +get-orig-source: + . debian/get-orig-source diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/debian/upstream b/debian/upstream new file mode 100644 index 0000000..75a35e5 --- /dev/null +++ b/debian/upstream @@ -0,0 +1,9 @@ +Reference: + Author: Franziska Zickmann and Martin S. Lindner and Bernhard Y. Renard + Title: "GIIRA—RNA-Seq driven gene finding incorporating ambiguous reads" + Journal: Bioinformatics + Year: 2013 + DOI: 10.1093/bioinformatics/btt577 + PMID: 24123675 + URL: http://bioinformatics.oxfordjournals.org/content/early/2013/10/26/bioinformatics.btt577 + eprint: http://bioinformatics.oxfordjournals.org/content/early/2013/10/26/bioinformatics.btt577.full.pdf+html diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..3946ee4 --- /dev/null +++ b/debian/watch @@ -0,0 +1,5 @@ +version=3 +# unfortunately watch files does not work since upstream has no version numbers +# see http://sourceforge.net/projects/giira/files/GIIRA/ +# +# http://sf.net/giira/GIIRA-([0-9.]+)\.(?:tgz|tar\.gz|tar\.xz|tar\.bz2|zip) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/giira.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
