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 <[email protected]> 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 <[email protected]> +Uploaders: Andreas Tille <[email protected]> +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 <[email protected]> +Source: https://snpeff.svn.sourceforge.net/svnroot/snpeff/SnpEffect/trunk/ + +Files: * +Copyright: © 2008-2012, Pablo Cingolani <[email protected]> +License: LGPLv3 + +Files: debian/* +Copyright: © 2012 Andreas Tille <[email protected]> +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
