[med-svn] r12514 - in trunk/packages: . snpeff snpeff/trunk snpeff/trunk/debian snpeff/trunk/debian/source

Wed Nov 7 21:08:21 UTC 2012

Author: tille
Date: 2012-11-07 21:08:20 +0000 (Wed, 07 Nov 2012)
New Revision: 12514

Added:
   trunk/packages/snpeff/
   trunk/packages/snpeff/trunk/
   trunk/packages/snpeff/trunk/debian/
   trunk/packages/snpeff/trunk/debian/changelog
   trunk/packages/snpeff/trunk/debian/compat
   trunk/packages/snpeff/trunk/debian/control
   trunk/packages/snpeff/trunk/debian/copyright
   trunk/packages/snpeff/trunk/debian/rules
   trunk/packages/snpeff/trunk/debian/source/
   trunk/packages/snpeff/trunk/debian/source/format
   trunk/packages/snpeff/trunk/debian/upstream
   trunk/packages/snpeff/trunk/debian/watch
Log:
Add machine readable files for snpEff which looks like a quite interesting but rather complex target.  A get-orig-source target that fetches SVN export needs to be written.


Added: trunk/packages/snpeff/trunk/debian/changelog
===================================================================

--- trunk/packages/snpeff/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/snpeff/trunk/debian/changelog	2012-11-07 21:08:20 UTC (rev 12514)
@@ -0,0 +1,5 @@
+snpeff (3.1-1) UNRELEASED; urgency=low
+
+  * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org>  Wed, 07 Nov 2012 17:01:35 +0100

Added: trunk/packages/snpeff/trunk/debian/compat
===================================================================
--- trunk/packages/snpeff/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/snpeff/trunk/debian/compat	2012-11-07 21:08:20 UTC (rev 12514)
@@ -0,0 +1 @@
+9

Added: trunk/packages/snpeff/trunk/debian/control
===================================================================
--- trunk/packages/snpeff/trunk/debian/control	                        (rev 0)
+++ trunk/packages/snpeff/trunk/debian/control	2012-11-07 21:08:20 UTC (rev 12514)
@@ -0,0 +1,27 @@
+Source: snpeff
+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: http://snpeff.sourceforge.net/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/snpeff/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/snpeff/trunk/
+
+Package: snpeff
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: annotation and effect prediction tool for genome sequences
+ SnpEff is a variant annotation and effect prediction tool. It annotates
+ and predicts the effects of variants on genes (such as amino acid
+ changes). 
+ .
+ The inputs are predicted variants (SNPs, insertions, deletions and
+ MNPs). The input file is usually obtained as a result of a sequencing
+ experiment, and it is usually in variant call format (VCF).
+ .
+ SnpEff analyzes the input variants. It annotates the variants and
+ calculates the effects they produce on known genes (e.g. amino acid
+ changes). A list of effects and annotations that SnpEff can calculate
+ can be found here. 

Added: trunk/packages/snpeff/trunk/debian/copyright
===================================================================
--- trunk/packages/snpeff/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/snpeff/trunk/debian/copyright	2012-11-07 21:08:20 UTC (rev 12514)
@@ -0,0 +1,29 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: snpEff
+Upstream-Contact: Pablo Cingolani <pcingola at users.sourceforge.net>
+Source: https://snpeff.svn.sourceforge.net/svnroot/snpeff/SnpEffect/trunk/
+
+Files: *
+Copyright: © 2008-2012, Pablo Cingolani <pcingola at users.sourceforge.net>
+License: LGPLv3
+
+Files: debian/*
+Copyright: © 2012 Andreas Tille <tille at debian.org>
+License: LGPLv3
+
+License: LGPLv3
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser 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.
+ .
+ You should have received a copy of the GNU Lesser General Public License
+ along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ .
+ On a Debian GNU/Linux system, the GNU Lesser GPL license version 3 is included
+ in the file ‘/usr/share/common-licenses/LGPL-3’.

Added: trunk/packages/snpeff/trunk/debian/rules
===================================================================
--- trunk/packages/snpeff/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/snpeff/trunk/debian/rules	2012-11-07 21:08:20 UTC (rev 12514)
@@ -0,0 +1,10 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+	dh $@
+
+get-orig-source:
+	# Need to write a script fetching an export from
+	#   https://snpeff.svn.sourceforge.net/svnroot/snpeff/SnpEffect/trunk/


Property changes on: trunk/packages/snpeff/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/snpeff/trunk/debian/source/format
===================================================================
--- trunk/packages/snpeff/trunk/debian/source/format	                        (rev 0)
+++ trunk/packages/snpeff/trunk/debian/source/format	2012-11-07 21:08:20 UTC (rev 12514)
@@ -0,0 +1 @@
+3.0 (quilt)

Added: trunk/packages/snpeff/trunk/debian/upstream
===================================================================
--- trunk/packages/snpeff/trunk/debian/upstream	                        (rev 0)
+++ trunk/packages/snpeff/trunk/debian/upstream	2012-11-07 21:08:20 UTC (rev 12514)
@@ -0,0 +1,12 @@
+Reference:
+  Author: Pablo Cingolani and Adrian Platts and Le Lily Wang and Melissa Coon and Tung Nguyen and Luan Wang and Susan J. Land and Douglas M. Ruden and Xiangyi Lu
+  Title: "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w^1118; iso-2; iso-3"
+  Journal: Fly
+  Year: 2012
+  Volume: 6
+  Number: 2
+  Pages: 80-92
+  DOI: 10.4161/fly.19695
+  PMID: 22728672
+  URL: http://www.landesbioscience.com/journals/fly/article/19695/
+  eprint: http://snpeff.sourceforge.net/SnpEff_paper.pdf

Added: trunk/packages/snpeff/trunk/debian/watch
===================================================================
--- trunk/packages/snpeff/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/snpeff/trunk/debian/watch	2012-11-07 21:08:20 UTC (rev 12514)
@@ -0,0 +1,7 @@
+version=3
+## This unfortunately only fetches the binary distribution
+## The source code is only available in SVN
+##   https://snpeff.svn.sourceforge.net/svnroot/snpeff/SnpEffect/trunk/
+#
+#opts="uversionmangle=s/_/./g" \
+# http://sf.net/snpeff/snpEff_v([\d._]+)_core\.zip


