velvet (1.2.10+dfsg1-5) unstable; urgency=medium [ Steffen Moeller ] * debian/upstream/metadata: Added references to registries. [ Andreas Tille ] * drop unneeded get-orig-source target * debhelper 11 (--no-parallel needed) * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.4 * d/control: Drop unnecessary Testsuite field * Provide manpages for versions with MAXKMERLENGTH = 127 * Try better hardening but failed (hints are welcome) * Fix spelling * Secure URI in watch file * Remove unused lintian override -- Andreas Tille Thu, 05 Jul 2018 10:17:41 +0200 velvet (1.2.10+dfsg1-4) experimental; urgency=medium * Add version with MAXKMERLENGTH=127 -- Andreas Tille Fri, 24 Feb 2017 10:10:36 +0100 velvet (1.2.10+dfsg1-3) unstable; urgency=medium * Moved from SVN to Git * Do not mention files in d/copyright that are not part of the source * Lintian override for false positives -- Andreas Tille Thu, 10 Dec 2015 09:02:23 +0100 velvet (1.2.10+dfsg1-2) unstable; urgency=medium * Fix gcc-5 build issue by adapting upstream patch Closes: #778161 * cme fix dpkg-control -- Andreas Tille Sat, 27 Jun 2015 11:44:54 +0200 velvet (1.2.10+dfsg1-1) unstable; urgency=medium * Drop more stuff from upstream source via Files-Excluded * cme fix dpkg-control * Do not pack example data into another archive * add autopkgtest (using new binary package velvet-tests) * do not create manpages at package build time (which is error prone anyway but rather prepare them before using debian/createmanpages script -- Andreas Tille Mon, 30 Jun 2014 13:56:46 +0200 velvet (1.2.10+dfsg-1biolinux6) trusty; urgency=medium [ Andreas Tille ] * Moved debian/upstream to debian/upstream/metadata * Base get-orig-source target on recent uscan that understands Files-Excluded * debian/rules: no need to explicitly force xz compression any more [ Tim Booth ] * Remove MeteVelvet and VelvetOptimiser in dh_clean, not dh_install * Include example_data.tar.xz in -example package -- Tim Booth Mon, 30 Jun 2014 11:39:24 +0100 velvet (1.2.10+dfsg-1biolinux5) trusty; urgency=low * Rebuild for Ubuntu Trusty * Fold in some chages from Bio-Linux * Add velvet-long package as suggested by upstream * Fix TeX deps so manual still builds * Add .c/.h and .pl files to dh_compress exclusions * Ensure that MetaVelvet and VelvetOptimiser sources are excluded as they don't belong in -examples -- Tim Booth Fri, 27 Jun 2014 13:52:48 +0100 velvet (1.2.10+dfsg-1) unstable; urgency=low * New upstream version (+adapted patch) * debian/watch: cope with +dfsg suffix (in addition to old ~nozlibcopy) * debian/get-orig-source: - Enable simple changing of suffix for repackaged source - Check for existence of enhanced uscan and use it if available for easier repackaging * debian/control: - cme fix dpkg-control - no explicit quilt Build-Depends (also removed from rules) - bumped python from Recommends to Depends because there are Python scripts installed in velvet/contrib - use anonscm in Vcs fields * debian/copyright: Add Files-Excluded to document what was removed from original source * rename debian/{docs,install} to debian/velvet.{docs,install} which is more safe in the case of multibinary package * debian/velvet.install: shuffle* files are in contrib directory now * debhelper 9 (control+compat) to enable hardening options * debian/rules: propagate hardening options * debian/copyright: - Files-Excluded: Exclude MAXOS internal files cruft from upstream archive - Adapt Source location * debian/README.source: Updated explanation for repackaging, droped some outdated information * debian/rules: - Do not try to rmdir nonexisting directory - Remove extra copies of GPL * debian/velvet-examples.install: use install instead of examples to move the examples into /usr/share/doc/velvet directly. Also all contrib stuff was moved here to not bloat main velvet binary package with potentially unused stuff in /usr/share * debian/README.Debian: document move of contrib stuff -- Andreas Tille Thu, 01 Aug 2013 14:33:28 +0200 velvet (1.2.03~nozlibcopy-1) unstable; urgency=low * New upstream release. * Updated debian/patches/include_debians_zlib.patch. -- Charles Plessy Thu, 16 Feb 2012 13:37:19 +0900 velvet (1.1.07~nozlibcopy-1) unstable; urgency=low * New upstream release (Closes: #647415). * debian/contol: - Pre-Depends on dpkg (>= 1.15.6) for Ubuntu LTS. - Removed Multi-Arch: foreign. -- Charles Plessy Fri, 09 Dec 2011 14:07:58 +0900 velvet (1.1.06~nozlibcopy-1) unstable; urgency=low [ Andreas Tille ] * New upstream version * debian/copyright: Revised * debian/get-orig-source: Do not remove MetaVelvet * debian/control: Build-Depends: texlive-latex-base [ Charles Plessy ] * Corrected VCS URLs in debian/control. * Compress source and binary packages with xz (debian/rules, debian/get-orig-source). * Turn on multithreading with OpenMP (debian/rules). * Remove empty directory contrib/MetaVelvet-v0.3.1/obj (debian/rules). -- Charles Plessy Tue, 27 Sep 2011 15:12:41 +0900 velvet (1.1.05-1ubuntu4) lucid; urgency=low * Moved from CDBS to DH * New upstream. Still includes a copy of Zlib but the default is now to use the system version, so removed relevant patch. * Modified build to work on unmodified upstream (still works on pruned upstream). -- Tim Booth Thu, 11 Aug 2011 13:34:46 +0100 velvet (1.1.02~nozlibcopy-1) unstable; urgency=low * New upstream version upgraded patches, tweak $(LIBS) into Z_LIB_FILES variable of Makefile which makes patch more robust against upstream changes * Debhelper 8 (control+compat) * debian/rules: Leave out Z_LIB_FILES in parameter list * debian/get-orig-source: Once we are rebuilding the original tarball anyway it makes sense to remove an outdated copy of MetaVelvet and replace it rather by a hint to the currently maintained source in README.source * Standards-Version: 3.9.2 (no changes needed) -- Andreas Tille Fri, 15 Apr 2011 10:51:16 +0200 velvet (1.0.18~nozlibcopy-1) unstable; urgency=low * New upstream version * debian/get-orig-source: Make sure MD5sum stays the same for different download -- Andreas Tille Wed, 19 Jan 2011 08:48:19 +0100 velvet (1.0.15~nozlibcopy-2) unstable; urgency=low * Fix FTBFS with ld --as-needed (thanks for the patch to Matthias Klose) Closes: #607535 -- Andreas Tille Mon, 20 Dec 2010 08:43:16 +0100 velvet (1.0.15~nozlibcopy-1) unstable; urgency=low * New upstream source * Standards-Version: 3.9.1 (no changes needed) * debian/get-upstream-source: Remove precompiled *.o files and .DS_Store files once we are repackaging anyway * debian/patches/fix-perl-path.patch: Fix Perl path -- Andreas Tille Wed, 24 Nov 2010 15:42:33 +0100 velvet (1.0.02~nozlibcopy-1) unstable; urgency=low * New upstream version * Source format 3.0 (quilt) * debian/control: - Recommends: python (some new scripts in /usr/share/velvet/contrib are Python scripts) - Build-Depends: quilt * debian/rules: include /usr/share/cdbs/1/rules/patchsys-quilt.mk (instead of simple-patchsys) * debian/patches: Switch to quilt * debian/patches/shuffleSequences_fasta.patch: Add interpreter to Python script -- Andreas Tille Thu, 24 Jun 2010 15:41:53 +0200 velvet (0.7.61~nozlibcopy-1) unstable; urgency=low * New upstream version * debian/get-orig-source, debian/rules: Strip zlib copy from upstream tarball -- Andreas Tille Mon, 22 Mar 2010 15:41:53 +0100 velvet (0.7.59~nozlibcopy-1) unstable; urgency=low * New upstream release [ Charles Plessy ] * Incremented Standard-Version in debian/control to reflect conformance with Policy 3.8.4 (no changes needed). [ Andreas Tille ] * Fixed watch file to make sure it is not supporting newer upstream -- Charles Plessy Sat, 20 Feb 2010 13:00:13 +0900 velvet (0.7.56~nozlibcopy-1) unstable; urgency=low * New upstream version. * Repackaged the upstream directory to remove the convenience copy of the zlib. Documented this in ‘debian/README.source’. Closes: #561433. * Updated debian/copyright. * Added ‘include_debians_zlib.patch’ to enforce the use of /usr/include/zlib.h. This patch is applied using CDBS, see ‘debian/rules’ and ‘debian/README.source’. * Renamed ‘debian/reference’ ‘debian/upstream-metadata.yaml’ and centralised upstream-specific information there. -- Charles Plessy Mon, 25 Jan 2010 13:03:06 +0900 velvet (0.7.55-1) unstable; urgency=low * New upstream version -- Andreas Tille Fri, 25 Sep 2009 14:52:41 +0200 velvet (0.7.53-1) unstable; urgency=low * New upstream release: - Ignored reads in Pebble corrected - Added automatic measure of median coverage and median insert length - Updated manual to cover the above -- Charles Plessy Fri, 04 Sep 2009 13:42:22 +0900 velvet (0.7.52-1) unstable; urgency=low * New upstream release: V 0.7.51 - Small parsing bug - Correction to the observed-insert-length script - Verified strncpy calls - NCBI friendly 10bp N-gaps V 0.7.52 - Crashing bug when parsing fa.gz files - Crashing bug with tiny Graph files - Bug when loading FASTA files with short lines - Corrected snp_view.pl script to write reverse strand reads in snp_view_reads file - Corrected snp_view.pl script to behave better near the edges of contigs - Updated observed_insert_length to compute the standard deviation of the set - Corrected observed_insert_length script so that it does not crash on empty libraries - Crashing bug when providing an odd number of paired reads - Mapping bug of reads during tour bus correction * Replaced the UNRELEASED tag by ‘unstable’ in debian/changelog as 0.7.50-1 was really uploaded and accepted by the archive. -- Charles Plessy Thu, 03 Sep 2009 20:00:54 +0900 velvet (0.7.50-1) unstable; urgency=low * New upstream release: V 0.7.49 - Added the optional output of unused reads - Added David Studholme's FastA -> AGP script V 0.7.50 - Added the extractContigReads script - Updated the FastA -> AGP script - Added the observed-insert-length script - Small parsing bug in simplified read import * Incremented Standards-Version in debian/control to reflect conformance with Policy 3.8.3 (no changes needed). -- Charles Plessy Wed, 19 Aug 2009 21:58:49 +0900 velvet (0.7.48-1) unstable; urgency=low * New upstream release: - Accelerated concatenation (pre-graph and graph) - Unlimited contig size - Bug in parsing FASTA files with very long lines - Parsing bug in snp_view.pl script -- Charles Plessy Tue, 11 Aug 2009 19:54:03 +0900 velvet (0.7.47-1) unstable; urgency=low * New upstream release correcting bugs and enhancing documentation. * Multi-Arch support (‘foreign’) in debian/control. * Corrected debian/install to avoid ugly ‘contrib/contrib’ location. -- Charles Plessy Thu, 30 Jul 2009 13:43:13 +0900 velvet (0.7.44-1) unstable; urgency=low * New upstream release. * Added bibliographic information in BibTeX format in debian/references. * debian/rules: touch zlib to avoid third-party zlib to be built. * Removed ‘debian/patches/20_external_zlib.patch’. Passing apropriate variables in debian/rules is enough to build dynamically on Debian's zlib. * Removed the quilt patch system (debian/control, debian/README.source debian/rules). * Incremented Standards-Version in debian/control to reflect conformance with Policy 3.8.2 (no changes needed). * Corrected the installation of files that were moved from the ‘third-party’ directory to the ‘contrib’ directory. * Experimentation on debian/copyright. -- Charles Plessy Sun, 12 Jul 2009 00:24:56 +0900 velvet (0.7.37-1) unstable; urgency=low * New upstream release. - Small formatting change to error messages - K > 31 now possible - --help option corrected for velvetg - Acceleration of k-mer operations (comparable to 64bit int performance) - Fixed variable lengths - Reordered struct declaration for more efficent memory alignment * debian/rules: - Restored manpage generation for velvetg*. - Added forgotten CFLAGS for the colorspace building. -- Charles Plessy Sat, 27 Jun 2009 12:27:27 +0900 velvet (0.7.34-1) unstable; urgency=low * New upstream release correcting multiple bugs, changing the stats output, allowing optional scaffolding and multiple rounds of Pebble. * Added the programs velveth_de and velvetg_de to the package in /usr/bin, and the scripts shuffleSequences_fasta.pl and shuffleSequences_fastq.pl in /usr/share/velvet (debian/rules, debian/install). * Refreshed debian/copyright. * Temporarly disabled the manpage generation of velvetg* because the --help option is not available (debian/rules). -- Charles Plessy Tue, 09 Jun 2009 21:28:03 +0900 velvet (0.7.31-1) unstable; urgency=low * New upstream version * Standards-Version: 3.8.1 (no changes needed) * Create manpages using help2man * Move third-party/layout and third-party/afg_handling to examples because these scripts are actually not to run velvet but for the convenience of users - in /urs/share/velvet these scripts seem to be perfectly hidden and in /usr/share/doc/velvet might create users attendance * Added missing quilt entry in debian/rules -- Andreas Tille Fri, 27 Mar 2009 13:23:32 +0100 velvet (0.7.24-1) unstable; urgency=low * Initial release (Closes: #487026) -- Charles Plessy Wed, 09 Jul 2008 14:06:55 +0900