Author: plessy Date: 2011-10-22 09:42:06 +0000 (Sat, 22 Oct 2011) New Revision: 8263
Added: trunk/packages/last-align/tags/189-1/ trunk/packages/last-align/tags/189-1/debian/changelog trunk/packages/last-align/tags/189-1/debian/control trunk/packages/last-align/tags/189-1/debian/copyright trunk/packages/last-align/tags/189-1/debian/rules Removed: trunk/packages/last-align/tags/189-1/debian/changelog trunk/packages/last-align/tags/189-1/debian/control trunk/packages/last-align/tags/189-1/debian/copyright trunk/packages/last-align/tags/189-1/debian/rules Log: [svn-buildpackage] Tagging last-align 189-1 Deleted: trunk/packages/last-align/tags/189-1/debian/changelog =================================================================== --- trunk/packages/last-align/trunk/debian/changelog 2011-10-22 04:54:32 UTC (rev 8260) +++ trunk/packages/last-align/tags/189-1/debian/changelog 2011-10-22 09:42:06 UTC (rev 8263) @@ -1,227 +0,0 @@ -last-align (184-1) unstable; urgency=low - - * New upstream release. - * Corrected VCS URLs (debian/control). - * Compress source and binary package with xz - (debian/get-orig-source, debian/rules). - - -- Charles Plessy <[email protected]> Sat, 17 Sep 2011 20:31:16 +0900 - -last-align (178-1) unstable; urgency=low - - * New upstream release changing format of lastal output (r177). - - -- Charles Plessy <[email protected]> Thu, 30 Jun 2011 13:53:03 +0900 - -last-align (171-1) unstable; urgency=low - - * New upstream release accepting gcc-4.6.patch (LP: #770770). - - Deleted debian/patches and its contents. - * Install changelog through CDBS (debian/rules, debian/docs). - * Proofread debian/copyright and refreshed DEP-5 format. - - -- Charles Plessy <[email protected]> Mon, 16 May 2011 22:01:53 +0900 - -last-align (162-1) unstable; urgency=low - - * New upstream version - * Standards-Version: 3.9.2 (no changes needed) - * debian/patches/gcc-4.6.patch: Fix gcc-4.6 build error - Closes: #625084 - - -- Andreas Tille <[email protected]> Mon, 02 May 2011 15:29:14 +0200 - -last-align (159-1) unstable; urgency=low - - * New upstream version - * Debhelper 8 (control+compat) - * debian/last-align.doc-base.last-align-manual: last-manual - seems to have dropped in favour of last-tutorial and other - smaller files - * debian/rules: Call help2man for new additional script - - -- Andreas Tille <[email protected]> Fri, 11 Mar 2011 23:29:44 +0100 - -last-align (146-1) unstable; urgency=low - - * New upstream version - * debian/rules: - - Maf2html is not any more in the source so we need not to create - the manpage - - Use help2man to create maf-cull manpage - - Remove src/lastex in clean target - - -- Andreas Tille <[email protected]> Thu, 25 Nov 2010 19:46:56 +0100 - -last-align (139-1) unstable; urgency=low - - * New upstream version - * Standards-Version: 3.9.1 (no changes needed) - - -- Andreas Tille <[email protected]> Wed, 17 Nov 2010 11:22:38 +0100 - -last-align (128-1) unstable; urgency=low - - * New upstream version - * Standards-Version: 3.9.0 (no changes needed) - - -- Andreas Tille <[email protected]> Fri, 09 Jul 2010 12:12:04 +0200 - -last-align (119-1) unstable; urgency=low - - [ Charles Plessy ] - * New upstream version. - * debian/rules get-orig-source: - * Pass --best and --no-name to gzip, for reproductible MD5 sums. - * Add ‘.orig’ to the repacked directory, to conform with the Debian - Developer’s Reference (§ 6.7.8.2.4). - * Build-depend on help2man (>= 1.36.4+nmu1), since the option - --version-string is not available earlier. - * Added missing empty line in debian/NEWS. - * Gathered information about upstream in debian/upstream-metadata.yaml. - - [ Andreas Tille ] - * debian/last-align.doc-base.last-align-lastex: - Upstream documentation evalue-tables.txt was replaced by lastex.txt - * debain/rules: - Added help2man call for maf-convert - - -- Andreas Tille <[email protected]> Thu, 24 Jun 2010 11:41:46 +0200 - -last-align (102-1) unstable; urgency=low - - * New upstream version - * debian/rules: scripts/maf2tab.py was removed -> do not try to - create manpage for this script - * debian/source/format: 3.0 (quilt) - - -- Andreas Tille <[email protected]> Mon, 29 Mar 2010 12:29:16 +0200 - -last-align (99-1) unstable; urgency=low - - * New upstream version - - -- Andreas Tille <[email protected]> Thu, 11 Mar 2010 15:38:23 +0100 - -last-align (96-1) unstable; urgency=low - - * New upstream version - * Standards-Version: 3.8.4 (no changes needed) - - -- Andreas Tille <[email protected]> Thu, 18 Feb 2010 14:43:15 +0100 - -last-align (87-1) unstable; urgency=low - - * New upstream version - - -- Andreas Tille <[email protected]> Tue, 03 Nov 2009 10:47:02 +0100 - -last-align (70-1) unstable; urgency=low - - * New upstream version - * Removed quilt dependency because upstream has applied patches - * help2man for all scripts - TODO: Write real manpages using the comments inside the scripts. - Upstream confirmed that there are no immediate plans for further - changes so writing static man pages seems to make sense - - -- Andreas Tille <[email protected]> Mon, 05 Oct 2009 11:56:25 +0200 - -last-align (62-1) unstable; urgency=low - - * New upstream version - * debian/control: - - Added myself to upstream - - Standards-Version: 3.8.3 - - Build-Depends: help2man, quilt, python-imaging - - Recommends: python-imaging - * debian/rules: Try to create manpages via help2man wherever possible - * debian/patches: Make sure help output goes to stdout as GNU coding - style suggests and is needed by help2man - - -- Andreas Tille <[email protected]> Tue, 29 Sep 2009 13:38:57 +0200 - -last-align (58-1) unstable; urgency=low - - * New upstream release able to use sequence quality scores. - - -- Charles Plessy <[email protected]> Fri, 19 Jun 2009 20:47:02 +0900 - -last-align (52-1) unstable; urgency=low - - * New upstream releases (52 and 51). - - Added maf2html.py: converts MAF-format alignments to coloured HTML format. - - Made lastal gapped extension faster, by removing an assert (surprising). - - Bugfix: made last-dotplot.py not crash on small sequences. - - -- Charles Plessy <[email protected]> Mon, 18 May 2009 23:52:24 +0900 - -last-align (50-1) unstable; urgency=low - - * New upstream release (minor changes). - - -- Charles Plessy <[email protected]> Tue, 21 Apr 2009 09:59:54 +0900 - -last-align (48-1) unstable; urgency=low - - * New upstream release. - - maf-join.py: joins pairwise alignments into multiple alignments. - - Changed lastal default gap existence cost for DNA to 7. - - Changed lastal default gapped score threshold for DNA to 40. - - maf-swap.py: Added -n option to move any sequence to the top. - - Allow suffixes K(ibibyte), M(ebibyte), and G(ibibyte) for sizes. - - Plus other bugfixes and improvements, please refer Upstream's changelog. - * Incremented Standards-Version in debian/control to reflect conformance - with Policy 3.8.1 (no changes needed). - * Simplified machine-readable debian/copyright file. - * last-align.doc-base.last-align-scripts: last-scripts.txt is now compressed. - - -- Charles Plessy <[email protected]> Wed, 08 Apr 2009 19:31:28 +0900 - -last-align (42-1) unstable; urgency=low - - * New upstream release: - - Corrects an overflow error that made lastal discard some gapped - alignments. - - Allows lastal options to be set in the score-matrix file. - * debian/copyright refreshed and points directly to GPLv3. - * Corrected the description in debian/control to not use - the first person. - - -- Charles Plessy <[email protected]> Tue, 10 Mar 2009 19:46:32 +0900 - -last-align (39-1) unstable; urgency=low - - * New upstream release. - - Bugfix: for protein alignments, tyrosine was forbidden in initial - matches. - - *Old lastdb protein databases won't work properly: you need to re-run - lastdb.* - * Added debian/NEWS.Debian to indicate the backward incompatibility. - * Debian/changelog: removed vanity entries and incremented copyright year. - * Transferred informations about packaging practices and repository from - README.source to README.Debian. - - -- Charles Plessy <[email protected]> Mon, 02 Feb 2009 12:42:26 +0900 - -last-align (37-1) unstable; urgency=low - - * New upstream release. - - Updated the documentation, including a table of optimal spaced seeds. - - Made lastdb bucket-making code slightly simpler & faster. - - Enabled reading & writing of huge files (at least on one system with - Linux-2.6.13/x86_64/gcc-4.0.2). - - Made lastdb radix sort a bit faster, with the oracle array trick. - - Allowed the mismatch score to be zero, due to a request. - - Made gaped extension faster for short sequences (e.g. tag mapping). - - Bugfix: the sequence names weren't printed correctly for - match-counting output (-j 0). - - Fixed compiler warnings with gcc 4.3. - - -- Charles Plessy <[email protected]> Sun, 28 Dec 2008 12:49:05 +0100 - -last-align (31-1) unstable; urgency=low - - * Initial release (Closes: #498562) - - -- Charles Plessy <[email protected]> Thu, 13 Nov 2008 15:44:31 +0900 Copied: trunk/packages/last-align/tags/189-1/debian/changelog (from rev 8262, trunk/packages/last-align/trunk/debian/changelog) =================================================================== --- trunk/packages/last-align/tags/189-1/debian/changelog (rev 0) +++ trunk/packages/last-align/tags/189-1/debian/changelog 2011-10-22 09:42:06 UTC (rev 8263) @@ -0,0 +1,241 @@ +last-align (189-1) unstable; urgency=low + + * New upstream release. + * Autogenerate a manual page for last-merge-batches (debian/rules). + + -- Charles Plessy <[email protected]> Sat, 22 Oct 2011 18:32:17 +0900 + +last-align (184-1ubuntu1) precise; urgency=low + + * Pre-Depends: dpkg (>= 1.15.6) for xz compression support. Needed until + after Ubuntu 12.04 LTS. + + -- Colin Watson <[email protected]> Mon, 17 Oct 2011 21:40:04 +0100 + +last-align (184-1) unstable; urgency=low + + * New upstream release. + * Corrected VCS URLs (debian/control). + * Compress source and binary package with xz + (debian/get-orig-source, debian/rules). + + -- Charles Plessy <[email protected]> Sat, 17 Sep 2011 20:31:16 +0900 + +last-align (178-1) unstable; urgency=low + + * New upstream release changing format of lastal output (r177). + + -- Charles Plessy <[email protected]> Thu, 30 Jun 2011 13:53:03 +0900 + +last-align (171-1) unstable; urgency=low + + * New upstream release accepting gcc-4.6.patch (LP: #770770). + - Deleted debian/patches and its contents. + * Install changelog through CDBS (debian/rules, debian/docs). + * Proofread debian/copyright and refreshed DEP-5 format. + + -- Charles Plessy <[email protected]> Mon, 16 May 2011 22:01:53 +0900 + +last-align (162-1) unstable; urgency=low + + * New upstream version + * Standards-Version: 3.9.2 (no changes needed) + * debian/patches/gcc-4.6.patch: Fix gcc-4.6 build error + Closes: #625084 + + -- Andreas Tille <[email protected]> Mon, 02 May 2011 15:29:14 +0200 + +last-align (159-1) unstable; urgency=low + + * New upstream version + * Debhelper 8 (control+compat) + * debian/last-align.doc-base.last-align-manual: last-manual + seems to have dropped in favour of last-tutorial and other + smaller files + * debian/rules: Call help2man for new additional script + + -- Andreas Tille <[email protected]> Fri, 11 Mar 2011 23:29:44 +0100 + +last-align (146-1) unstable; urgency=low + + * New upstream version + * debian/rules: + - Maf2html is not any more in the source so we need not to create + the manpage + - Use help2man to create maf-cull manpage + - Remove src/lastex in clean target + + -- Andreas Tille <[email protected]> Thu, 25 Nov 2010 19:46:56 +0100 + +last-align (139-1) unstable; urgency=low + + * New upstream version + * Standards-Version: 3.9.1 (no changes needed) + + -- Andreas Tille <[email protected]> Wed, 17 Nov 2010 11:22:38 +0100 + +last-align (128-1) unstable; urgency=low + + * New upstream version + * Standards-Version: 3.9.0 (no changes needed) + + -- Andreas Tille <[email protected]> Fri, 09 Jul 2010 12:12:04 +0200 + +last-align (119-1) unstable; urgency=low + + [ Charles Plessy ] + * New upstream version. + * debian/rules get-orig-source: + * Pass --best and --no-name to gzip, for reproductible MD5 sums. + * Add ‘.orig’ to the repacked directory, to conform with the Debian + Developer’s Reference (§ 6.7.8.2.4). + * Build-depend on help2man (>= 1.36.4+nmu1), since the option + --version-string is not available earlier. + * Added missing empty line in debian/NEWS. + * Gathered information about upstream in debian/upstream-metadata.yaml. + + [ Andreas Tille ] + * debian/last-align.doc-base.last-align-lastex: + Upstream documentation evalue-tables.txt was replaced by lastex.txt + * debain/rules: + Added help2man call for maf-convert + + -- Andreas Tille <[email protected]> Thu, 24 Jun 2010 11:41:46 +0200 + +last-align (102-1) unstable; urgency=low + + * New upstream version + * debian/rules: scripts/maf2tab.py was removed -> do not try to + create manpage for this script + * debian/source/format: 3.0 (quilt) + + -- Andreas Tille <[email protected]> Mon, 29 Mar 2010 12:29:16 +0200 + +last-align (99-1) unstable; urgency=low + + * New upstream version + + -- Andreas Tille <[email protected]> Thu, 11 Mar 2010 15:38:23 +0100 + +last-align (96-1) unstable; urgency=low + + * New upstream version + * Standards-Version: 3.8.4 (no changes needed) + + -- Andreas Tille <[email protected]> Thu, 18 Feb 2010 14:43:15 +0100 + +last-align (87-1) unstable; urgency=low + + * New upstream version + + -- Andreas Tille <[email protected]> Tue, 03 Nov 2009 10:47:02 +0100 + +last-align (70-1) unstable; urgency=low + + * New upstream version + * Removed quilt dependency because upstream has applied patches + * help2man for all scripts + TODO: Write real manpages using the comments inside the scripts. + Upstream confirmed that there are no immediate plans for further + changes so writing static man pages seems to make sense + + -- Andreas Tille <[email protected]> Mon, 05 Oct 2009 11:56:25 +0200 + +last-align (62-1) unstable; urgency=low + + * New upstream version + * debian/control: + - Added myself to upstream + - Standards-Version: 3.8.3 + - Build-Depends: help2man, quilt, python-imaging + - Recommends: python-imaging + * debian/rules: Try to create manpages via help2man wherever possible + * debian/patches: Make sure help output goes to stdout as GNU coding + style suggests and is needed by help2man + + -- Andreas Tille <[email protected]> Tue, 29 Sep 2009 13:38:57 +0200 + +last-align (58-1) unstable; urgency=low + + * New upstream release able to use sequence quality scores. + + -- Charles Plessy <[email protected]> Fri, 19 Jun 2009 20:47:02 +0900 + +last-align (52-1) unstable; urgency=low + + * New upstream releases (52 and 51). + - Added maf2html.py: converts MAF-format alignments to coloured HTML format. + - Made lastal gapped extension faster, by removing an assert (surprising). + - Bugfix: made last-dotplot.py not crash on small sequences. + + -- Charles Plessy <[email protected]> Mon, 18 May 2009 23:52:24 +0900 + +last-align (50-1) unstable; urgency=low + + * New upstream release (minor changes). + + -- Charles Plessy <[email protected]> Tue, 21 Apr 2009 09:59:54 +0900 + +last-align (48-1) unstable; urgency=low + + * New upstream release. + - maf-join.py: joins pairwise alignments into multiple alignments. + - Changed lastal default gap existence cost for DNA to 7. + - Changed lastal default gapped score threshold for DNA to 40. + - maf-swap.py: Added -n option to move any sequence to the top. + - Allow suffixes K(ibibyte), M(ebibyte), and G(ibibyte) for sizes. + - Plus other bugfixes and improvements, please refer Upstream's changelog. + * Incremented Standards-Version in debian/control to reflect conformance + with Policy 3.8.1 (no changes needed). + * Simplified machine-readable debian/copyright file. + * last-align.doc-base.last-align-scripts: last-scripts.txt is now compressed. + + -- Charles Plessy <[email protected]> Wed, 08 Apr 2009 19:31:28 +0900 + +last-align (42-1) unstable; urgency=low + + * New upstream release: + - Corrects an overflow error that made lastal discard some gapped + alignments. + - Allows lastal options to be set in the score-matrix file. + * debian/copyright refreshed and points directly to GPLv3. + * Corrected the description in debian/control to not use + the first person. + + -- Charles Plessy <[email protected]> Tue, 10 Mar 2009 19:46:32 +0900 + +last-align (39-1) unstable; urgency=low + + * New upstream release. + - Bugfix: for protein alignments, tyrosine was forbidden in initial + matches. + - *Old lastdb protein databases won't work properly: you need to re-run + lastdb.* + * Added debian/NEWS.Debian to indicate the backward incompatibility. + * Debian/changelog: removed vanity entries and incremented copyright year. + * Transferred informations about packaging practices and repository from + README.source to README.Debian. + + -- Charles Plessy <[email protected]> Mon, 02 Feb 2009 12:42:26 +0900 + +last-align (37-1) unstable; urgency=low + + * New upstream release. + - Updated the documentation, including a table of optimal spaced seeds. + - Made lastdb bucket-making code slightly simpler & faster. + - Enabled reading & writing of huge files (at least on one system with + Linux-2.6.13/x86_64/gcc-4.0.2). + - Made lastdb radix sort a bit faster, with the oracle array trick. + - Allowed the mismatch score to be zero, due to a request. + - Made gaped extension faster for short sequences (e.g. tag mapping). + - Bugfix: the sequence names weren't printed correctly for + match-counting output (-j 0). + - Fixed compiler warnings with gcc 4.3. + + -- Charles Plessy <[email protected]> Sun, 28 Dec 2008 12:49:05 +0100 + +last-align (31-1) unstable; urgency=low + + * Initial release (Closes: #498562) + + -- Charles Plessy <[email protected]> Thu, 13 Nov 2008 15:44:31 +0900 Deleted: trunk/packages/last-align/tags/189-1/debian/control =================================================================== --- trunk/packages/last-align/trunk/debian/control 2011-10-22 04:54:32 UTC (rev 8260) +++ trunk/packages/last-align/tags/189-1/debian/control 2011-10-22 09:42:06 UTC (rev 8263) @@ -1,31 +0,0 @@ -Source: last-align -Section: science -Priority: optional -Maintainer: Debian Med Packaging Team <[email protected]> -DM-Upload-Allowed: yes -Uploaders: Charles Plessy <[email protected]>, - Andreas Tille <[email protected]> -Build-Depends: debhelper (>= 8), cdbs, help2man (>= 1.36.4+nmu1), python-imaging -Standards-Version: 3.9.2 -Homepage: http://last.cbrc.jp/ -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/last-align/ -Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/last-align/trunk/ - -Package: last-align -Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends} -Recommends: python, python-imaging -Description: genome-scale comparison of biological sequences - LAST is software for comparing and aligning sequences, typically DNA or - protein sequences. LAST is similar to BLAST, but it copes better with very - large amounts of sequence data. Here are two things LAST is good at: - . - * Comparing large (e.g. mammalian) genomes. - * Mapping lots of sequence tags onto a genome. - . - The main technical innovation is that LAST finds initial matches based on - their multiplicity, instead of using a fixed size (e.g. BLAST uses 10-mers). - This allows one to map tags to genomes without repeat-masking, without becoming - overwhelmed by repetitive hits. To find these variable-sized matches, it uses - a suffix array (inspired by Vmatch). To achieve high sensitivity, it uses a - discontiguous suffix array, analogous to spaced seeds. Copied: trunk/packages/last-align/tags/189-1/debian/control (from rev 8261, trunk/packages/last-align/trunk/debian/control) =================================================================== --- trunk/packages/last-align/tags/189-1/debian/control (rev 0) +++ trunk/packages/last-align/tags/189-1/debian/control 2011-10-22 09:42:06 UTC (rev 8263) @@ -0,0 +1,32 @@ +Source: last-align +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Charles Plessy <[email protected]>, + Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 8), cdbs, help2man (>= 1.36.4+nmu1), python-imaging +Standards-Version: 3.9.2 +Homepage: http://last.cbrc.jp/ +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/last-align/ +Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/last-align/trunk/ + +Package: last-align +Architecture: any +Pre-Depends: dpkg (>= 1.15.6) +Depends: ${shlibs:Depends}, ${misc:Depends} +Recommends: python, python-imaging +Description: genome-scale comparison of biological sequences + LAST is software for comparing and aligning sequences, typically DNA or + protein sequences. LAST is similar to BLAST, but it copes better with very + large amounts of sequence data. Here are two things LAST is good at: + . + * Comparing large (e.g. mammalian) genomes. + * Mapping lots of sequence tags onto a genome. + . + The main technical innovation is that LAST finds initial matches based on + their multiplicity, instead of using a fixed size (e.g. BLAST uses 10-mers). + This allows one to map tags to genomes without repeat-masking, without becoming + overwhelmed by repetitive hits. To find these variable-sized matches, it uses + a suffix array (inspired by Vmatch). To achieve high sensitivity, it uses a + discontiguous suffix array, analogous to spaced seeds. Deleted: trunk/packages/last-align/tags/189-1/debian/copyright =================================================================== --- trunk/packages/last-align/trunk/debian/copyright 2011-10-22 04:54:32 UTC (rev 8260) +++ trunk/packages/last-align/tags/189-1/debian/copyright 2011-10-22 09:42:06 UTC (rev 8263) @@ -1,71 +0,0 @@ -Format: http://dep.debian.net/deps/dep5/ -Source: http://last.cbrc.jp/archive/last-184.zip - -Files: * -Copyright: © 2008–2011 Martin C. Frith, Michiaki Hamada and Paul B. Horton <[email protected]> -License: GPL-3+ -Comment: On Debian systems the full text of the GNU General Public License - can be found in the `/usr/share/common-licenses/GPL-3' file. - -Files: CA_code/* -Copyright: not copyrighted -License: public-domain - Public domain code from Yi-Kuo Yu & Stephen Altschul, NCBI - -Files: src/gumbel_params/* -Copyright: not copyrighted -License: public-domain - PUBLIC DOMAIN NOTICE - National Center for Biotechnology Information - . - This software/database is a "United States Government Work" under the - terms of the United States Copyright Act. It was written as part of - the author's offical duties as a United States Government employee and - thus cannot be copyrighted. This software/database is freely available - to the public for use. The National Library of Medicine and the U.S. - Government have not placed any restriction on its use or reproduction. - . - Although all reasonable efforts have been taken to ensure the accuracy - and reliability of the software and data, the NLM and the U.S. - Government do not and cannot warrant the performance or results that - may be obtained by using this software or data. The NLM and the U.S. - Government disclaim all warranties, express or implied, including - warranties of performance, merchantability or fitness for any particular - purpose. - . - Please cite the author in any work or product based on this material. - -Files: CA_code/lambda_calculator.c -Copyright: © 2008 Michiaki Hamada -License: GPL-3+ -Comment: Adapted from public domain code by Yi-Kuo Yu, NCBI - -Files: CA_code/lambda_calculator.h -Copyright: © 2008 Michiaki Hamada -License: GPL-3+ - -Files: src/Xdrop3FrameAligner.hh - src/Xdrop3FrameAligner.cc - /src/GeneticCode.hh -Copyright: © 2009 Toshiyuki Sato -License: GPL-3+ - -Files: debian/* -Copyright: © 2008–2009,2011 Charles Plessy <[email protected]> -License: Same - Same as LAST itself (See above). - -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. - . - You should have received a copy of the GNU General Public License - along with this program. If not, see <http://www.gnu.org/licenses/>. - Copied: trunk/packages/last-align/tags/189-1/debian/copyright (from rev 8262, trunk/packages/last-align/trunk/debian/copyright) =================================================================== --- trunk/packages/last-align/tags/189-1/debian/copyright (rev 0) +++ trunk/packages/last-align/tags/189-1/debian/copyright 2011-10-22 09:42:06 UTC (rev 8263) @@ -0,0 +1,71 @@ +Format: http://dep.debian.net/deps/dep5/ +Source: http://last.cbrc.jp/archive/last-189.zip + +Files: * +Copyright: © 2008–2011 Martin C. Frith, Michiaki Hamada and Paul B. Horton <[email protected]> +License: GPL-3+ +Comment: On Debian systems the full text of the GNU General Public License + can be found in the `/usr/share/common-licenses/GPL-3' file. + +Files: CA_code/* +Copyright: not copyrighted +License: public-domain + Public domain code from Yi-Kuo Yu & Stephen Altschul, NCBI + +Files: src/gumbel_params/* +Copyright: not copyrighted +License: public-domain + PUBLIC DOMAIN NOTICE + National Center for Biotechnology Information + . + This software/database is a "United States Government Work" under the + terms of the United States Copyright Act. It was written as part of + the author's offical duties as a United States Government employee and + thus cannot be copyrighted. This software/database is freely available + to the public for use. The National Library of Medicine and the U.S. + Government have not placed any restriction on its use or reproduction. + . + Although all reasonable efforts have been taken to ensure the accuracy + and reliability of the software and data, the NLM and the U.S. + Government do not and cannot warrant the performance or results that + may be obtained by using this software or data. The NLM and the U.S. + Government disclaim all warranties, express or implied, including + warranties of performance, merchantability or fitness for any particular + purpose. + . + Please cite the author in any work or product based on this material. + +Files: CA_code/lambda_calculator.c +Copyright: © 2008 Michiaki Hamada +License: GPL-3+ +Comment: Adapted from public domain code by Yi-Kuo Yu, NCBI + +Files: CA_code/lambda_calculator.h +Copyright: © 2008 Michiaki Hamada +License: GPL-3+ + +Files: src/Xdrop3FrameAligner.hh + src/Xdrop3FrameAligner.cc + /src/GeneticCode.hh +Copyright: © 2009 Toshiyuki Sato +License: GPL-3+ + +Files: debian/* +Copyright: © 2008–2009,2011 Charles Plessy <[email protected]> +License: Same + Same as LAST itself (See above). + +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. + . + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + Deleted: trunk/packages/last-align/tags/189-1/debian/rules =================================================================== --- trunk/packages/last-align/trunk/debian/rules 2011-10-22 04:54:32 UTC (rev 8260) +++ trunk/packages/last-align/tags/189-1/debian/rules 2011-10-22 09:42:06 UTC (rev 8263) @@ -1,71 +0,0 @@ -#!/usr/bin/make -f - -# This package is maintained by the Debian Med packaging team. Please refer to -# our group policy if you would like to commit to our Subversion repository. All -# Debian developpers have write acces to it. -# -# http://debian-med.alioth.debian.org/docs/policy.html - -include /usr/share/cdbs/1/rules/debhelper.mk -# include /usr/share/cdbs/1/rules/patchsys-quilt.mk -include /usr/share/cdbs/1/class/makefile.mk - -DEB_MAKE_BUILD_TARGET = --directory src -DEB_INSTALL_CHANGELOGS_ALL = ChangeLog.txt -DEB_DH_BUILDDEB_ARGS = -- -Z xz - -pkg=last-align -version=$(shell dpkg-parsechangelog -ldebian/changelog | grep Version: | cut -f2 -d' ' | cut -f1 -d- ) -mandir=$(CURDIR)/debian/$(pkg)/usr/share/man/man1/ - -clean:: - $(RM) src/lastdb src/lastal src/lastex src/*.o - -binary-fixup/$(pkg):: - prename 's/.py$$//' debian/$(pkg)/usr/bin/*py - prename 's/.sh$$//' debian/$(pkg)/usr/bin/*sh - -# try to create man pages whereever possible -build/$(pkg):: - mkdir -p $(mandir) - help2man --no-info --name='make a dotplot, a.k.a. Oxford Grid, of alignments in LAST tabular format' \ - --version-string="$(version)" \ - $(CURDIR)/scripts/last-dotplot.py > $(mandir)/last-dotplot.1 - help2man --no-info --name="genome-scale comparison of biological sequences" \ - --version-string="$(version)" --help-option="-h" \ - $(CURDIR)/src/lastal > $(mandir)/lastal.1 - help2man --no-info --name="genome-scale comparison of biological sequences" \ - --version-string="$(version)" --help-option="-h" \ - $(CURDIR)/src/lastdb > $(mandir)/lastdb.1 - help2man --no-info --version-string="$(version)" \ - --name="Sort MAF-format alignments by sequence name" \ - $(CURDIR)/scripts/maf-sort.sh > $(mandir)/maf-sort.1 - help2man --no-info --version-string="$(version)" \ - --name="changes the order of the sequences in MAF-format alignments" \ - $(CURDIR)/scripts/maf-swap.py > $(mandir)/maf-swap.1 - help2man --no-info --version-string="$(version)" \ - --name="Add extra column with mapping probabilities" \ - $(CURDIR)/scripts/last-map-probs.py > $(mandir)/last-map-probs.1 - help2man --no-info --version-string="$(version)" \ - --name="Clean up MAF-format alignments" \ - $(CURDIR)/scripts/last-reduce-alignments.sh > $(mandir)/last-reduce-alignments.1 - help2man --no-info --version-string="$(version)" \ - --name='Remove MAF-format alignments which are "dominated" by others' \ - $(CURDIR)/scripts/last-remove-dominated.py > $(mandir)/last-remove-dominated.1 - help2man --no-info --version-string="$(version)" \ - --name="Join two or more sets of MAF-format multiple alignments" \ - $(CURDIR)/scripts/maf-join.py > $(mandir)/maf-join.1 - help2man --no-info --version-string="$(version)" \ - --name="Convert MAF-format alignments to tabular format" \ - $(CURDIR)/scripts/maf-convert.py > $(mandir)/maf-convert.1 - help2man --no-info --version-string="$(version)" \ - --name="Cull alignments whose top\-sequence coordinates are contained in LIMIT or more" \ - $(CURDIR)/scripts/maf-cull.py > $(mandir)/maf-cull.1 - help2man --no-info --version-string="$(version)" \ - --name="Read alignments of paired DNA reads to a genome" \ - $(CURDIR)/scripts/last-pair-probs.py > $(mandir)/last-pair-probs.1 - -# The unzip command from the unzip package is needed for this one. -# This target obtains the latest upstream version and not the latest packaged version -get-orig-source: - . debian/get-orig-source Copied: trunk/packages/last-align/tags/189-1/debian/rules (from rev 8262, trunk/packages/last-align/trunk/debian/rules) =================================================================== --- trunk/packages/last-align/tags/189-1/debian/rules (rev 0) +++ trunk/packages/last-align/tags/189-1/debian/rules 2011-10-22 09:42:06 UTC (rev 8263) @@ -0,0 +1,74 @@ +#!/usr/bin/make -f + +# This package is maintained by the Debian Med packaging team. Please refer to +# our group policy if you would like to commit to our Subversion repository. All +# Debian developpers have write acces to it. +# +# http://debian-med.alioth.debian.org/docs/policy.html + +include /usr/share/cdbs/1/rules/debhelper.mk +# include /usr/share/cdbs/1/rules/patchsys-quilt.mk +include /usr/share/cdbs/1/class/makefile.mk + +DEB_MAKE_BUILD_TARGET = --directory src +DEB_INSTALL_CHANGELOGS_ALL = ChangeLog.txt +DEB_DH_BUILDDEB_ARGS = -- -Z xz + +pkg=last-align +version=$(shell dpkg-parsechangelog -ldebian/changelog | grep Version: | cut -f2 -d' ' | cut -f1 -d- ) +mandir=$(CURDIR)/debian/$(pkg)/usr/share/man/man1/ + +clean:: + $(RM) src/lastdb src/lastal src/lastex src/*.o + +binary-fixup/$(pkg):: + prename 's/.py$$//' debian/$(pkg)/usr/bin/*py + prename 's/.sh$$//' debian/$(pkg)/usr/bin/*sh + +# try to create man pages whereever possible +build/$(pkg):: + mkdir -p $(mandir) + help2man --no-info --name='make a dotplot, a.k.a. Oxford Grid, of alignments in LAST tabular format' \ + --version-string="$(version)" \ + $(CURDIR)/scripts/last-dotplot.py > $(mandir)/last-dotplot.1 + help2man --no-info --name="genome-scale comparison of biological sequences" \ + --version-string="$(version)" --help-option="-h" \ + $(CURDIR)/src/lastal > $(mandir)/lastal.1 + help2man --no-info --name="genome-scale comparison of biological sequences" \ + --version-string="$(version)" --help-option="-h" \ + $(CURDIR)/src/lastdb > $(mandir)/lastdb.1 + help2man --no-info --version-string="$(version)" \ + --name="Sort MAF-format alignments by sequence name" \ + $(CURDIR)/scripts/maf-sort.sh > $(mandir)/maf-sort.1 + help2man --no-info --version-string="$(version)" \ + --name="changes the order of the sequences in MAF-format alignments" \ + $(CURDIR)/scripts/maf-swap.py > $(mandir)/maf-swap.1 + help2man --no-info --version-string="$(version)" \ + --name="Add extra column with mapping probabilities" \ + $(CURDIR)/scripts/last-map-probs.py > $(mandir)/last-map-probs.1 + help2man --no-info --version-string="$(version)" \ + --name="Read files of lastal output, merge corresponding batches, and write them." \ + $(CURDIR)/scripts/last-merge-batches.py > $(mandir)/last-merge-batches.1 + help2man --no-info --version-string="$(version)" \ + --name="Clean up MAF-format alignments" \ + $(CURDIR)/scripts/last-reduce-alignments.sh > $(mandir)/last-reduce-alignments.1 + help2man --no-info --version-string="$(version)" \ + --name='Remove MAF-format alignments which are "dominated" by others' \ + $(CURDIR)/scripts/last-remove-dominated.py > $(mandir)/last-remove-dominated.1 + help2man --no-info --version-string="$(version)" \ + --name="Join two or more sets of MAF-format multiple alignments" \ + $(CURDIR)/scripts/maf-join.py > $(mandir)/maf-join.1 + help2man --no-info --version-string="$(version)" \ + --name="Convert MAF-format alignments to tabular format" \ + $(CURDIR)/scripts/maf-convert.py > $(mandir)/maf-convert.1 + help2man --no-info --version-string="$(version)" \ + --name="Cull alignments whose top\-sequence coordinates are contained in LIMIT or more" \ + $(CURDIR)/scripts/maf-cull.py > $(mandir)/maf-cull.1 + help2man --no-info --version-string="$(version)" \ + --name="Read alignments of paired DNA reads to a genome" \ + $(CURDIR)/scripts/last-pair-probs.py > $(mandir)/last-pair-probs.1 + +# The unzip command from the unzip package is needed for this one. +# This target obtains the latest upstream version and not the latest packaged version +get-orig-source: + . debian/get-orig-source _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
