[med-svn] [giira] 01/01: Inject initial debian/ dir
Andreas Tille
tille at debian.org
Fri Feb 7 23:07:40 UTC 2014
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 <tille at debian.org>
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 <tille at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+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 <ZickmannF at rki.de>
+Source: http://sourceforge.net/projects/giira/files/
+
+Files: *
+Copyright: 2013 Franziska Zickmann <ZickmannF at rki.de>
+ Robert Koch-Institut
+License: GPLv3
+
+Files: debian/*
+Copyright: 2014 Andreas Tille <tille at debian.org>
+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)
--
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