Author: plessy Date: 2009-10-07 05:13:24 +0000 (Wed, 07 Oct 2009) New Revision: 4180
Added: trunk/packages/bwa/trunk/debian/ trunk/packages/bwa/trunk/debian/changelog trunk/packages/bwa/trunk/debian/compat trunk/packages/bwa/trunk/debian/control trunk/packages/bwa/trunk/debian/copyright trunk/packages/bwa/trunk/debian/docs trunk/packages/bwa/trunk/debian/install trunk/packages/bwa/trunk/debian/manpages trunk/packages/bwa/trunk/debian/rules trunk/packages/bwa/trunk/debian/upstream-metadata.yaml trunk/packages/bwa/trunk/debian/watch Log: [svn-inject] Applying Debian modifications to trunk Property changes on: trunk/packages/bwa/trunk/debian ___________________________________________________________________ Added: mergeWithUpstream + 1 Added: trunk/packages/bwa/trunk/debian/changelog =================================================================== --- trunk/packages/bwa/trunk/debian/changelog (rev 0) +++ trunk/packages/bwa/trunk/debian/changelog 2009-10-07 05:13:24 UTC (rev 4180) @@ -0,0 +1,5 @@ +bwa (0.5.3-1) UNRELEASED; urgency=low + + * Initial release (Closes: #548719) + + -- Charles Plessy <[email protected]> Mon, 28 Sep 2009 19:16:57 +0900 Added: trunk/packages/bwa/trunk/debian/compat =================================================================== --- trunk/packages/bwa/trunk/debian/compat (rev 0) +++ trunk/packages/bwa/trunk/debian/compat 2009-10-07 05:13:24 UTC (rev 4180) @@ -0,0 +1 @@ +7 Added: trunk/packages/bwa/trunk/debian/control =================================================================== --- trunk/packages/bwa/trunk/debian/control (rev 0) +++ trunk/packages/bwa/trunk/debian/control 2009-10-07 05:13:24 UTC (rev 4180) @@ -0,0 +1,23 @@ +Source: bwa +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Charles Plessy <[email protected]> +Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev +Standards-Version: 3.8.3 +Homepage: http://bio-bwa.sourceforge.net/ +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/bwa/trunk/?rev=0&sc=0 +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/bwa/trunk/ + +Package: bwa +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Suggests: samtools +Description: Burrows-Wheeler Aligner + Burrows-Wheeler Aligner (BWA) is a program that aligns relatively short + nucleotide sequences against a long reference sequence such as the human + genome. It implements two algorithms, bwa-short and dBWT-SW. The former works + for query sequences shorter than 200 bp and the latter for longer sequences up + to around 100 kbp. Both algorithms do gapped alignment. They are usually more + accurate and faster on queries with low error rates. Added: trunk/packages/bwa/trunk/debian/copyright =================================================================== --- trunk/packages/bwa/trunk/debian/copyright (rev 0) +++ trunk/packages/bwa/trunk/debian/copyright 2009-10-07 05:13:24 UTC (rev 4180) @@ -0,0 +1,63 @@ +Name : Burrows-Wheeler Aligner +Contact : [email protected] +Source : http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.3.tar.bz2 + +Copyright : © 2008 Genome Research Ltd (GRL) + 2008, by Heng Li <[email protected]> + © 2003-2006, 2008, 2009, by Heng Li <[email protected]> + © 2008, by Attractive Chaos <[email protected]> + © 2008 Yuta Mori +License : MIT + + Permission is hereby granted, free of charge, to any person obtaining + a copy of this software and associated documentation files (the + "Software"), to deal in the Software without restriction, including + without limitation the rights to use, copy, modify, merge, publish, + distribute, sublicense, and/or sell copies of the Software, and to + permit persons to whom the Software is furnished to do so, subject to + the following conditions: + + The above copyright notice and this permission notice shall be + included in all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF + MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS + BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN + ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. + + +Files : bwt_gen/bwt_gen.* +Copyright : © 2004, Wong Chi Kwong +License : GPL-2+ + + 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 2 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 General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + +On Debian systems, you can find a copy of the GNU General Public License +version 2 in ‘/usr/share/common-licenses/GPL-2’. + + +Files : bwt_gen/QSufSort.* +Copyright : 1999, N. Jesper Larsson +License : + + This software may be used freely for any purpose. However, when distributed, + the original source must be clearly stated, and, when the source code is + distributed, the copyright notice must be retained and any alterations in + the code must be clearly marked. No warranty is given regarding the quality + of this software. Added: trunk/packages/bwa/trunk/debian/docs =================================================================== --- trunk/packages/bwa/trunk/debian/docs (rev 0) +++ trunk/packages/bwa/trunk/debian/docs 2009-10-07 05:13:24 UTC (rev 4180) @@ -0,0 +1,2 @@ +ChangeLog +NEWS Added: trunk/packages/bwa/trunk/debian/install =================================================================== --- trunk/packages/bwa/trunk/debian/install (rev 0) +++ trunk/packages/bwa/trunk/debian/install 2009-10-07 05:13:24 UTC (rev 4180) @@ -0,0 +1,3 @@ +bwa usr/bin +# A different solid2fastq.pl script is present in the maq package. +solid2fastq.pl usr/share/bwa Added: trunk/packages/bwa/trunk/debian/manpages =================================================================== --- trunk/packages/bwa/trunk/debian/manpages (rev 0) +++ trunk/packages/bwa/trunk/debian/manpages 2009-10-07 05:13:24 UTC (rev 4180) @@ -0,0 +1 @@ +bwa.1 Added: trunk/packages/bwa/trunk/debian/rules =================================================================== --- trunk/packages/bwa/trunk/debian/rules (rev 0) +++ trunk/packages/bwa/trunk/debian/rules 2009-10-07 05:13:24 UTC (rev 4180) @@ -0,0 +1,4 @@ +#!/usr/bin/make -f + +include /usr/share/cdbs/1/rules/debhelper.mk +include /usr/share/cdbs/1/class/makefile.mk Property changes on: trunk/packages/bwa/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/bwa/trunk/debian/upstream-metadata.yaml =================================================================== --- trunk/packages/bwa/trunk/debian/upstream-metadata.yaml (rev 0) +++ trunk/packages/bwa/trunk/debian/upstream-metadata.yaml 2009-10-07 05:13:24 UTC (rev 4180) @@ -0,0 +1,17 @@ +DOI: 10.1093/bioinformatics/btp324 +Homepage: http://bio-bwa.sourceforge.net/ +PMID: 19451168 +Reference: | + @article{HengLi07152009, + author = {Li, Heng and Durbin, Richard}, + title = {{Fast and accurate short read alignment with Burrows-Wheeler transform}}, + journal = {Bioinformatics}, + volume = {25}, + number = {14}, + pages = {1754-1760}, + doi = {10.1093/bioinformatics/btp324}, + year = {2009}, + URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/14/1754}, + eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/25/14/1754.pdf} +} +Repository: https://bio-bwa.svn.sourceforge.net/svnroot/bio-bwa Added: trunk/packages/bwa/trunk/debian/watch =================================================================== --- trunk/packages/bwa/trunk/debian/watch (rev 0) +++ trunk/packages/bwa/trunk/debian/watch 2009-10-07 05:13:24 UTC (rev 4180) @@ -0,0 +1,2 @@ +version=3 +http://sf.net/bio-bwa/bwa-(.*)\.tar\.bz2 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
