debian/0000755000000000000000000000000011675367277007213 5ustar debian/watch0000644000000000000000000000011211110210412010170 0ustar version=3 http://www.imsc.res.in/~rsidd/sigma/ source/sigma-(.*)\.tar\.gz debian/copyright0000644000000000000000000000262011646107217011126 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://www.imsc.res.in/~rsidd/sigma/source/sigma-1.1.3.tar.gz Files: * Copyright: Rahul Siddharthan, 2006-2009 License: GPL-2+ This package 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 package 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 package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA Comment: On Debian systems, the complete text of the GNU General Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'. Files: debian/* Copyright: 2006–2009 Charles Plessy 2008 Andreas Tille 2008 Nelson Antônio de Oliveira 2008 David Paleino License: PD Please treat this work as if it were under public domain. debian/manpages0000644000000000000000000000001011176077112010676 0ustar sigma.1 debian/changelog0000644000000000000000000000573011675367123011060 0ustar sigma-align (1.1.3-3) unstable; urgency=low * Fix bug in long description Closes: #652922 -- Andreas Tille Sat, 24 Dec 2011 16:22:30 +0100 sigma-align (1.1.3-2) unstable; urgency=low [ Charles Plessy ] * Documented information in ‘debian/upstream-metadata.yaml’. * Converted debian/copyright to machine-readable format version 1.0. [Steffen Möller] * Split long description in two (Closes: #644663) [ Andreas Tille ] * debian/control: - Fixed Vcs fields - Standards-Version incremented to reflect compliance with Policy 3.9.2. - Long description less than 80 characters per line * Source format 3.0 (quilt) * debian/rules: dh instead of cdbs * Debhelper 8 (control+compat) -- Andreas Tille Fri, 16 Dec 2011 15:45:30 +0100 sigma-align (1.1.3-1) unstable; urgency=low * New upstream release. * Converted the packaging to CDBS. - debian/rules is much shorter. - CDBS will take care of updating config.guess and config.sub. - Created debian/docs and debian/manpages. * debian/control: - Updated my email address. - Incremented Standards-Version to reflect conformance with Policy 3.8.1 (no changes needed). - Depend on debhelper 7, cdbs and autotools-dev - Moved bibliographic information to debian/reference. - Use nice Unicode English quotes in the long descriptions. * debian/copyright: - Updated to latest version of the machine-readable format. - Incremented years and updated my email address. * Using debhelper 7 (debian/compat). -- Charles Plessy Mon, 27 Apr 2009 20:49:06 +0900 sigma-align (1.1.1-3) unstable; urgency=low [ Nelson A. de Oliveira ] * Added watch file. [ David Paleino ] * debian/rules: failsafe $(MAKE) distclean. * Updated to Standards-Version 3.7.3 (no changes needed) [ Charles Plessy ] * debian/control: - Moved the Homepage: field out from the package's description. - Updated the VCS fields by removing their XS- prefix. - Suppressed an unclear sentence from the description. [ Andreas Tille ] * Added myself to uploaders -- Andreas Tille Tue, 18 Mar 2008 12:10:00 +0100 sigma-align (1.1.1-2) unstable; urgency=low * Removed obsolete manpage in the debian directory. * Not rebuilding the manpage, and dropping corresponding build-dependencies. -- Charles Plessy Thu, 26 Jul 2007 23:02:07 +0900 sigma-align (1.1.1-1) unstable; urgency=low * New upstream release. - 1.1 : complete rewrite in C. - 1.1.1 : fixes a building problem on powerpc. * Manpage adopted and updated by the upstream author of Sigma. * Add Subversion repository URL to debian/control. -- Charles Plessy Sun, 8 Apr 2007 15:26:34 +0900 sigma-align (1.0-1) unstable; urgency=low * Initial release Closes: #378289 -- Charles Plessy Tue, 5 Sep 2006 23:14:46 +0900 debian/source/0000755000000000000000000000000011672654517010504 5ustar debian/source/format0000644000000000000000000000001411473514012011672 0ustar 3.0 (quilt) debian/compat0000644000000000000000000000000211672654670010402 0ustar 8 debian/rules0000755000000000000000000000006311672654755010267 0ustar #!/usr/bin/make -f %: dh $@ --with autotools_dev debian/reference0000644000000000000000000000054111176077112011052 0ustar @Article{16542424, AUTHOR = {Siddharthan, Rahul}, TITLE = {Sigma: multiple alignment of weakly-conserved non-coding DNA sequence}, JOURNAL = {BMC Bioinformatics}, VOLUME = {7}, YEAR = {2006}, NUMBER = {1}, PAGES = {143}, URL = {http://www.biomedcentral.com/1471-2105/7/143}, DOI = {10.1186/1471-2105-7-143}, PubMedID = {16542424}, ISSN = {1471-2105}, } debian/upstream-metadata.yaml0000644000000000000000000000074411326521302013470 0ustar Contact: Rahul Siddharthan DOI: 10.1186/1471-2105-7-143 Homepage: http://www.imsc.res.in/~rsidd/sigma/ PMID: 16542424 Name: Sigma Reference: AUTHOR: Siddharthan, Rahul TITLE: Sigma: multiple alignment of weakly-conserved non-coding DNA sequence JOURNAL: BMC Bioinformatics VOLUME: 7 YEAR: 2006 NUMBER: 1 PAGES: 143 URL: http://www.biomedcentral.com/1471-2105/7/143 ISSN: 1471-2105 Watch: http://www.imsc.res.in/~rsidd/sigma/ source/sigma-(.*)\.tar\.gz debian/control0000644000000000000000000000232211675367241010604 0ustar Source: sigma-align Section: science Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Charles Plessy , Andreas Tille Build-Depends: autotools-dev, debhelper (>= 8), libglib2.0-dev Standards-Version: 3.9.2 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/sigma-align/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/sigma-align/trunk/ Homepage: http://www.imsc.res.in/~rsidd/sigma/ Package: sigma-align Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: Simple greedy multiple alignment of non-coding DNA sequences Sigma (“Simple greedy multiple alignment”) is an alignment program. It's algorithm and scoring scheme are designed specifically for non-coding DNA sequence. . It uses a strategy of seeking the best possible gapless local alignments. This happens at each step making the best possible alignment consistent with existing alignments. It scores the significance of the alignment based on the lengths of the aligned fragments and a background model. These may be supplied or estimated from an auxiliary file of intergenic DNA. debian/docs0000644000000000000000000000001511176077112010040 0ustar README NOTES