[med-svn] [oases] 01/09: Inject machine readable files for oases packaging

[Andreas Tille]

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tille pushed a commit to branch master
in repository oases.

commit 02c468c2b8219a94d131b9e0bdc68e62121da40c
Author: Andreas Tille <tille at debian.org>
Date:   Wed Nov 7 15:06:06 2012 +0000

    Inject machine readable files for oases packaging
---
 debian/changelog     |  5 +++++
 debian/compat        |  1 +
 debian/control       | 21 +++++++++++++++++++++
 debian/copyright     | 26 ++++++++++++++++++++++++++
 debian/rules         |  6 ++++++
 debian/source/format |  1 +
 debian/upstream      | 12 ++++++++++++
 debian/watch         |  2 ++
 8 files changed, 74 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..88db2f2
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+oases (0.2.08-1) unstable; urgency=low
+
+  * Initial release (Closes: #<bug>)
+
+ -- DMPT <debian-med-packaging at lists.alioth.debian.org>  Thu, 24 May 2012 14:30:13 +0200
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..0c31f97
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,21 @@
+Source: oases
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.4
+Homepage: https://www.ebi.ac.uk/~zerbino/oases/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/oases/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/oases/trunk/
+
+Package: oases
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: de novo transcriptome assembler for very short reads
+ Oases is a de novo transcriptome assembler designed to produce
+ transcripts from short read sequencing technologies, such as Illumina,
+ SOLiD, or 454 in the absence of any genomic assembly.  Oases uploads a
+ preliminary assembly produced by Velvet, and clusters the contigs into
+ small groups, called loci. It then exploits the paired-end read and long
+ read information, when available, to construct transcript isoforms.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..588a88f
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,26 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: oases
+Source: https://www.ebi.ac.uk/~zerbino/oases/
+
+Files: *
+Copyright: © 2010-2011, Daniel Zerbino <dzerbino at soe.ucsc.edu>
+                        Marcel Schulz <marcel.schulz at molgen.mpg.de>
+License: GPL-3
+
+Files: debian/*
+Copyright: © 2012 Andreas Tille <tille at debian.org>
+License: GPL-3
+
+License: GPL-3
+ 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 a copy of the GNU General Public License
+ version 3 at /usr/share/common-licenses/GPL-3
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..6055261
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,6 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+	dh $@
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..e7c8556
--- /dev/null
+++ b/debian/upstream
@@ -0,0 +1,12 @@
+Reference:
+  Author: Marcel H. Schulz and Daniel R. Zerbino and Martin Vingron1 and Ewan Birney
+  Title: "Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels"
+  Journal: Bioinformatics
+  Year: 2012
+  Volume: 28
+  Number: 8
+  Pages:  1086-1092
+  DOI: 10.1093/bioinformatics/bts094
+  PMID: 22368243
+  URL: http://bioinformatics.oxfordjournals.org/content/28/8/1086
+  eprint: http://bioinformatics.oxfordjournals.org/content/28/8/1086.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..915899d
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,2 @@
+version=3
+http://www.ebi.ac.uk/~zerbino/oases/ oases_([\d.]+)\.tgz

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