[med-svn] r17755 - in trunk/packages/last-align/tags: . 475-1/debian
Charles Plessy
plessy at moszumanska.debian.org
Sat Aug 16 06:36:12 UTC 2014
Author: plessy
Date: 2014-08-16 06:36:12 +0000 (Sat, 16 Aug 2014)
New Revision: 17755
Added:
trunk/packages/last-align/tags/475-1/
trunk/packages/last-align/tags/475-1/debian/changelog
trunk/packages/last-align/tags/475-1/debian/control
trunk/packages/last-align/tags/475-1/debian/copyright
trunk/packages/last-align/tags/475-1/debian/rules
Removed:
trunk/packages/last-align/tags/475-1/debian/README.source
trunk/packages/last-align/tags/475-1/debian/changelog
trunk/packages/last-align/tags/475-1/debian/control
trunk/packages/last-align/tags/475-1/debian/copyright
trunk/packages/last-align/tags/475-1/debian/rules
Log:
[svn-buildpackage] Tagging last-align 475-1
Deleted: trunk/packages/last-align/tags/475-1/debian/README.source
===================================================================
--- trunk/packages/last-align/trunk/debian/README.source 2014-08-15 22:21:08 UTC (rev 17747)
+++ trunk/packages/last-align/tags/475-1/debian/README.source 2014-08-16 06:36:12 UTC (rev 17755)
@@ -1,3 +0,0 @@
-Upstream sources are distributed as a ZIP archive. The debian/rules file
-contains a rule named `get-orig-source' to create a gzipped tar archive whose
-name follows the Debian policy.
Deleted: trunk/packages/last-align/tags/475-1/debian/changelog
===================================================================
--- trunk/packages/last-align/trunk/debian/changelog 2014-08-15 22:21:08 UTC (rev 17747)
+++ trunk/packages/last-align/tags/475-1/debian/changelog 2014-08-16 06:36:12 UTC (rev 17755)
@@ -1,311 +0,0 @@
-last-align (418-1) unstable; urgency=medium
-
- * New upstream release
- * debian/upstream -> debian/upstream/metadata
-
- -- Andreas Tille <tille at debian.org> Fri, 21 Mar 2014 14:57:56 +0100
-
-last-align (393-1) unstable; urgency=medium
-
- * New upstream release
- * cme fix dpkg-control
- * debian/rules: Adapt help2man to the fact that two scripts were
- deleted from upstream source (no idea how to write manpages for the
- new parallel-* scripts)
- * Adapt doc-base control script (text file might be uncompressed)
-
- -- Andreas Tille <tille at debian.org> Tue, 28 Jan 2014 17:57:09 +0100
-
-last-align (359-1) unstable; urgency=low
-
- * New upstream release.
- * debian/control:
- - Removed Pre-Depends on dpkg as Ubuntu LTS is released.
- - Removed obsolete DM-Upload-Allowed field.
- - Use canonical VCS URLs.
- - Normalised with config-model-edit.
- - Removed version constraint on help2man, satisfied in oldstable.
- - Mark conformance with Policy version 3.9.4.
- * debian/watch: updated.
- * debian/rules:
- - Restore xz compression of the binary packages.
- - Produce a manual page for ‘last-split’ with help2man.
-
- -- Charles Plessy <plessy at debian.org> Sun, 06 Oct 2013 12:16:12 +0900
-
-last-align (199-1) unstable; urgency=low
-
- [ Charles Plessy ]
- * Summarise LAST license in debian/copyright header.
-
- [ Andreas Tille ]
- * New upstream version
- Closes: #667939
- * debian/rules:
- - switch from cdbs to dh
- - add help2man call for lastex
- * debian/install:
- - removed to use upstream install target (which also installs
- lastex)
- * debian/copyright: Make Source field more generic
-
- -- Andreas Tille <tille at debian.org> Mon, 07 May 2012 13:28:25 +0200
-
-last-align (198-1) unstable; urgency=low
-
- * New upstream version
- * debian/rules,debian/get-orig-source: Simplified downloading original
- source
- * debhelper 9 to enable hardening flags (control+compat, closes: #667939).
-
- -- Andreas Tille <tille at debian.org> Mon, 02 Apr 2012 14:16:35 +0200
-
-last-align (193-1) unstable; urgency=low
-
- * New upstream version
- * debian/upstream: Removed duplicate entries for DOI/PMID
- * debian/control: Standards-Version: 3.9.3 (no changes needed)
-
- -- Andreas Tille <tille at debian.org> Thu, 08 Mar 2012 14:34:36 +0100
-
-last-align (189-1) unstable; urgency=low
-
- * New upstream release.
- * Autogenerate a manual page for last-merge-batches (debian/rules).
-
- -- Charles Plessy <plessy at debian.org> 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 <cjwatson at ubuntu.com> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> Mon, 29 Mar 2010 12:29:16 +0200
-
-last-align (99-1) unstable; urgency=low
-
- * New upstream version
-
- -- Andreas Tille <tille at debian.org> 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 <tille at debian.org> Thu, 18 Feb 2010 14:43:15 +0100
-
-last-align (87-1) unstable; urgency=low
-
- * New upstream version
-
- -- Andreas Tille <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> Mon, 18 May 2009 23:52:24 +0900
-
-last-align (50-1) unstable; urgency=low
-
- * New upstream release (minor changes).
-
- -- Charles Plessy <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> Sun, 28 Dec 2008 12:49:05 +0100
-
-last-align (31-1) unstable; urgency=low
-
- * Initial release (Closes: #498562)
-
- -- Charles Plessy <plessy at debian.org> Thu, 13 Nov 2008 15:44:31 +0900
Copied: trunk/packages/last-align/tags/475-1/debian/changelog (from rev 17754, trunk/packages/last-align/trunk/debian/changelog)
===================================================================
--- trunk/packages/last-align/tags/475-1/debian/changelog (rev 0)
+++ trunk/packages/last-align/tags/475-1/debian/changelog 2014-08-16 06:36:12 UTC (rev 17755)
@@ -0,0 +1,322 @@
+last-align (475-1) unstable; urgency=medium
+
+ * New upstream release.
+ * debian/rules:
+ - removed compression command, as it is now the default.
+ - removed manual page of last-merge-batches.py.
+ * debian/control: suggest GNU parallel.
+ * debian/README.source: removed as conversion from zip is now automagic.
+
+ -- Charles Plessy <plessy at debian.org> Sat, 16 Aug 2014 15:20:37 +0900
+
+last-align (418-1) unstable; urgency=medium
+
+ * New upstream release
+ * debian/upstream -> debian/upstream/metadata
+
+ -- Andreas Tille <tille at debian.org> Fri, 21 Mar 2014 14:57:56 +0100
+
+last-align (393-1) unstable; urgency=medium
+
+ * New upstream release
+ * cme fix dpkg-control
+ * debian/rules: Adapt help2man to the fact that two scripts were
+ deleted from upstream source (no idea how to write manpages for the
+ new parallel-* scripts)
+ * Adapt doc-base control script (text file might be uncompressed)
+
+ -- Andreas Tille <tille at debian.org> Tue, 28 Jan 2014 17:57:09 +0100
+
+last-align (359-1) unstable; urgency=low
+
+ * New upstream release.
+ * debian/control:
+ - Removed Pre-Depends on dpkg as Ubuntu LTS is released.
+ - Removed obsolete DM-Upload-Allowed field.
+ - Use canonical VCS URLs.
+ - Normalised with config-model-edit.
+ - Removed version constraint on help2man, satisfied in oldstable.
+ - Mark conformance with Policy version 3.9.4.
+ * debian/watch: updated.
+ * debian/rules:
+ - Restore xz compression of the binary packages.
+ - Produce a manual page for ‘last-split’ with help2man.
+
+ -- Charles Plessy <plessy at debian.org> Sun, 06 Oct 2013 12:16:12 +0900
+
+last-align (199-1) unstable; urgency=low
+
+ [ Charles Plessy ]
+ * Summarise LAST license in debian/copyright header.
+
+ [ Andreas Tille ]
+ * New upstream version
+ Closes: #667939
+ * debian/rules:
+ - switch from cdbs to dh
+ - add help2man call for lastex
+ * debian/install:
+ - removed to use upstream install target (which also installs
+ lastex)
+ * debian/copyright: Make Source field more generic
+
+ -- Andreas Tille <tille at debian.org> Mon, 07 May 2012 13:28:25 +0200
+
+last-align (198-1) unstable; urgency=low
+
+ * New upstream version
+ * debian/rules,debian/get-orig-source: Simplified downloading original
+ source
+ * debhelper 9 to enable hardening flags (control+compat, closes: #667939).
+
+ -- Andreas Tille <tille at debian.org> Mon, 02 Apr 2012 14:16:35 +0200
+
+last-align (193-1) unstable; urgency=low
+
+ * New upstream version
+ * debian/upstream: Removed duplicate entries for DOI/PMID
+ * debian/control: Standards-Version: 3.9.3 (no changes needed)
+
+ -- Andreas Tille <tille at debian.org> Thu, 08 Mar 2012 14:34:36 +0100
+
+last-align (189-1) unstable; urgency=low
+
+ * New upstream release.
+ * Autogenerate a manual page for last-merge-batches (debian/rules).
+
+ -- Charles Plessy <plessy at debian.org> 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 <cjwatson at ubuntu.com> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> Mon, 29 Mar 2010 12:29:16 +0200
+
+last-align (99-1) unstable; urgency=low
+
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> 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 <tille at debian.org> Thu, 18 Feb 2010 14:43:15 +0100
+
+last-align (87-1) unstable; urgency=low
+
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> Mon, 18 May 2009 23:52:24 +0900
+
+last-align (50-1) unstable; urgency=low
+
+ * New upstream release (minor changes).
+
+ -- Charles Plessy <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> Sun, 28 Dec 2008 12:49:05 +0100
+
+last-align (31-1) unstable; urgency=low
+
+ * Initial release (Closes: #498562)
+
+ -- Charles Plessy <plessy at debian.org> Thu, 13 Nov 2008 15:44:31 +0900
Deleted: trunk/packages/last-align/tags/475-1/debian/control
===================================================================
--- trunk/packages/last-align/trunk/debian/control 2014-08-15 22:21:08 UTC (rev 17747)
+++ trunk/packages/last-align/tags/475-1/debian/control 2014-08-16 06:36:12 UTC (rev 17755)
@@ -1,34 +0,0 @@
-Source: last-align
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Charles Plessy <plessy at debian.org>,
- Andreas Tille <tille at debian.org>
-Section: science
-Priority: optional
-Build-Depends: debhelper (>= 9),
- help2man,
- python-imaging
-Standards-Version: 3.9.5
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/last-align/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/last-align/trunk/
-Homepage: http://last.cbrc.jp/
-
-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/475-1/debian/control (from rev 17749, trunk/packages/last-align/trunk/debian/control)
===================================================================
--- trunk/packages/last-align/tags/475-1/debian/control (rev 0)
+++ trunk/packages/last-align/tags/475-1/debian/control 2014-08-16 06:36:12 UTC (rev 17755)
@@ -0,0 +1,35 @@
+Source: last-align
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Charles Plessy <plessy at debian.org>,
+ Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ help2man,
+ python-imaging
+Standards-Version: 3.9.5
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/last-align/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/last-align/trunk/
+Homepage: http://last.cbrc.jp/
+
+Package: last-align
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Recommends: python,
+ python-imaging
+Suggests: parallel
+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/475-1/debian/copyright
===================================================================
--- trunk/packages/last-align/trunk/debian/copyright 2014-08-15 22:21:08 UTC (rev 17747)
+++ trunk/packages/last-align/tags/475-1/debian/copyright 2014-08-16 06:36:12 UTC (rev 17755)
@@ -1,66 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Source: http://last.cbrc.jp/last-359.zip
-License: GPL-3+
- LAST combines GPL-3+ and public domain programs, and links to libc6, libgcc1
- and libstdc++6. Its effective license as a whole is therefore GPL-3+.
-
-Files: *
-Copyright: © 2008–2013 Martin C. Frith
- © 2009–2013 Toshiyuki Sato
- © 2008–2011 Michiaki Hamada
- © 2012 Risa Kawaguchi
-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: 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/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.
-
-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/475-1/debian/copyright (from rev 17750, trunk/packages/last-align/trunk/debian/copyright)
===================================================================
--- trunk/packages/last-align/tags/475-1/debian/copyright (rev 0)
+++ trunk/packages/last-align/tags/475-1/debian/copyright 2014-08-16 06:36:12 UTC (rev 17755)
@@ -0,0 +1,66 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: http://last.cbrc.jp/last-475.zip
+License: GPL-3+
+ LAST combines GPL-3+ and public domain programs, and links to libc6, libgcc1
+ and libstdc++6. Its effective license as a whole is therefore GPL-3+.
+
+Files: *
+Copyright: © 2008–2014 Martin C. Frith
+ © 2009–2013 Toshiyuki Sato
+ © 2008–2011 Michiaki Hamada
+ © 2012 Risa Kawaguchi
+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: 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/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.
+
+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/475-1/debian/rules
===================================================================
--- trunk/packages/last-align/trunk/debian/rules 2014-08-15 22:21:08 UTC (rev 17747)
+++ trunk/packages/last-align/tags/475-1/debian/rules 2014-08-16 06:36:12 UTC (rev 17755)
@@ -1,86 +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
-
-pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
-version=$(shell dpkg-parsechangelog -ldebian/changelog | grep Version: | cut -f2 -d' ' | cut -f1 -d- )
-mandir=$(CURDIR)/debian/$(pkg)/usr/share/man/man1/
-
-# Copy upstream CXXFLAGS here because makefile enables only overriding them
-CXXFLAGS += -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic
-# -Wconversion
-# -fomit-frame-pointer ?
-
-%:
- dh $@
-
-override_dh_auto_build:
- make all CXXFLAGS="$(CXXFLAGS)" CFLAGS="$(CFLAGS)" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)"
-
-override_dh_auto_install:
- make install prefix=$(CURDIR)/debian/$(pkg)/usr
- prename 's/.py$$//' debian/$(pkg)/usr/bin/*py
- prename 's/.sh$$//' debian/$(pkg)/usr/bin/*sh
-
- # try to create man pages whereever possible
- 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 > $(mandir)/lastdb.1
- help2man --no-info --name="Calculate expected numbers of alignments for random sequences." \
- --version-string="$(version)" --help-option="-h" \
- $(CURDIR)/src/lastex > $(mandir)/lastex.1
- help2man --no-info --version-string="$(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 > $(mandir)/last-merge-batches.1
- # These scripts were droped
- #help2man --no-info --version-string="$(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='Estimates "split" or "spliced" alignments.' \
- $(CURDIR)/src/last-split > $(mandir)/last-split.1
- help2man --no-info --version-string="$(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
-
-override_dh_installchangelogs:
- dh_installchangelogs ChangeLog.txt
-
-override_dh_builddeb:
- dh_builddeb -- -Z xz
-
-get-orig-source:
- mkdir -p ../tarballs
- uscan --verbose --force-download --repack --rename --destdir=../tarballs
Copied: trunk/packages/last-align/tags/475-1/debian/rules (from rev 17752, trunk/packages/last-align/trunk/debian/rules)
===================================================================
--- trunk/packages/last-align/tags/475-1/debian/rules (rev 0)
+++ trunk/packages/last-align/tags/475-1/debian/rules 2014-08-16 06:36:12 UTC (rev 17755)
@@ -0,0 +1,89 @@
+#!/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
+
+pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
+version=$(shell dpkg-parsechangelog -ldebian/changelog | grep Version: | cut -f2 -d' ' | cut -f1 -d- )
+mandir=$(CURDIR)/debian/$(pkg)/usr/share/man/man1/
+
+# Copy upstream CXXFLAGS here because makefile enables only overriding them
+CXXFLAGS += -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic
+# -Wconversion
+# -fomit-frame-pointer ?
+
+%:
+ dh $@
+
+override_dh_auto_build:
+ make all CXXFLAGS="$(CXXFLAGS)" CFLAGS="$(CFLAGS)" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)"
+
+HELP2MAN = help2man --no-info --version-string="$(version)"
+
+override_dh_auto_install:
+ make install prefix=$(CURDIR)/debian/$(pkg)/usr
+ prename 's/.py$$//' debian/$(pkg)/usr/bin/*py
+ prename 's/.sh$$//' debian/$(pkg)/usr/bin/*sh
+
+ # try to create man pages whereever possible
+ mkdir -p $(mandir)
+ $(HELP2MAN) \
+ --name='make a dotplot, a.k.a. Oxford Grid, of alignments in LAST tabular format' \
+ $(CURDIR)/scripts/last-dotplot.py > $(mandir)/last-dotplot.1
+ $(HELP2MAN) \
+ --name="genome-scale comparison of biological sequences" \
+ --help-option="-h" \
+ $(CURDIR)/src/lastal > $(mandir)/lastal.1
+ $(HELP2MAN) \
+ --name="genome-scale comparison of biological sequences" \
+ --help-option="-h" \
+ $(CURDIR)/src/lastdb > $(mandir)/lastdb.1
+ $(HELP2MAN) \
+ --name="Calculate expected numbers of alignments for random sequences." \
+ --help-option="-h" \
+ $(CURDIR)/src/lastex > $(mandir)/lastex.1
+ $(HELP2MAN) \
+ --name="Sort MAF-format alignments by sequence name" \
+ $(CURDIR)/scripts/maf-sort.sh > $(mandir)/maf-sort.1
+ $(HELP2MAN) \
+ --name="changes the order of the sequences in MAF-format alignments" \
+ $(CURDIR)/scripts/maf-swap.py > $(mandir)/maf-swap.1
+ $(HELP2MAN) \
+ --name="Add extra column with mapping probabilities" \
+ $(CURDIR)/scripts/last-map-probs.py > $(mandir)/last-map-probs.1
+ # This script has not enough to put in a manual page.
+ #$(HELP2MAN) \
+ # --name="Read files of lastal output, merge corresponding batches, and write them." \
+ # $(CURDIR)/scripts/last-merge-batches.py > $(mandir)/last-merge-batches.1
+ # These scripts were droped
+ #$(HELP2MAN) \
+ # --name="Clean up MAF-format alignments" \
+ # $(CURDIR)/scripts/last-reduce-alignments.sh > $(mandir)/last-reduce-alignments.1
+ #$(HELP2MAN) \
+ # --name='Remove MAF-format alignments which are "dominated" by others' \
+ # $(CURDIR)/scripts/last-remove-dominated.py > $(mandir)/last-remove-dominated.1
+ $(HELP2MAN) \
+ --name='Estimates "split" or "spliced" alignments.' \
+ $(CURDIR)/src/last-split > $(mandir)/last-split.1
+ $(HELP2MAN) \
+ --name="Join two or more sets of MAF-format multiple alignments" \
+ $(CURDIR)/scripts/maf-join.py > $(mandir)/maf-join.1
+ $(HELP2MAN) \
+ --name="Convert MAF-format alignments to tabular format" \
+ $(CURDIR)/scripts/maf-convert.py > $(mandir)/maf-convert.1
+ $(HELP2MAN) \
+ --name="Cull alignments whose top\-sequence coordinates are contained in LIMIT or more" \
+ $(CURDIR)/scripts/maf-cull.py > $(mandir)/maf-cull.1
+ $(HELP2MAN) \
+ --name="Read alignments of paired DNA reads to a genome" \
+ $(CURDIR)/scripts/last-pair-probs.py > $(mandir)/last-pair-probs.1
+
+override_dh_installchangelogs:
+ dh_installchangelogs ChangeLog.txt
+
+get-orig-source:
+ mkdir -p ../tarballs
+ uscan --verbose --force-download --repack --rename --destdir=../tarballs
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