qiime (1.9.1+dfsg-2) unstable; urgency=medium [ Steffen Moeller ] * Introduced EDAM annotation to debian/upstream/edam. * debian/upstream/metadata: - Added references to registries - yamllint cleanliness [ Gianfranco Costamagna ] * Cherry-pick ubuntu fix, adding python-biom-format to build-dependencies [ Andreas Tille ] * Moved packaging from SVN to Git * debhelper 10 * cme fix dpkg-control * Standards-Version: 4.1.1 * Fix lintian-override about false positives * d/rules: do not parse d/changelog * hardening=+all * Fixing dependency relations (related to #820308): - qiime-default-reference: Depends -> Suggests - Build-Depends: bwa, infernal, raxml, sortmerna, swarm, vsearch - TODO: python-burrito-fillings, emperor -- Andreas Tille Fri, 17 Nov 2017 13:32:51 +0100 qiime (1.9.1+dfsg-1) unstable; urgency=medium * Take over changes from BioLinux for new upstream version * adapt d/watch and get-orig-source target to new uscan * cme fix dpkg-control * Remove denoiser from d/control since there is no such package any more * DEP5 fixes * Add lintian override for false positive about JS without source * Enable building arch independent packages separately Closes: #806101 * This upload also Closes: #758987 -- Andreas Tille Wed, 25 Nov 2015 17:07:33 +0100 qiime (1.9.1+dfsg-0ubuntu1) trusty; urgency=medium * New upstream - should be a bugfix upgrade * Attempt to re-sync Bio-Linux and Deb Med packages * Ensure we depend on correct biom-format version and ditto for burrito-fillings. * Add in manpages and print_qiime_config_all helper script * Remove link to king which is no longer used * Remove reference to expunged vb_viles -- Tim Booth Thu, 30 Jul 2015 10:17:08 +0100 qiime (1.9.0+dfsg-0biolinux5) trusty; urgency=medium * Fix /usr/bin/qiime (again) and update help for usearch -- Tim Booth Tue, 14 Apr 2015 13:53:26 +0100 qiime (1.9.0+dfsg-0biolinux4) trusty; urgency=medium * Remove symlink for King * Tweak qiime script so I can call "qiime print_qiime_config_all" directly * Add missing setuptools dep -- Tim Booth Mon, 09 Mar 2015 18:25:27 +0000 qiime (1.9.0+dfsg-0biolinux2) trusty; urgency=medium * New upstream * Use vSearch instead of uSearch * Use SumaClust, SortMeRNA and SeqPrep * Use latest RDP-classifier * Add dep on python-pandas and new package python-burrito-fillings * Add dep on qiime-default-reference * Remove usearch61 as we now call vsearch * Make help more helpful (I hope), by - Making the pseudo-manpage into a real manpage - Adding a print_qiime_config_all script * New patch to allow RDP-Classifier to not be retrained by default * Dep on Emperor 0.9.51 * Dep on new biom-format * No more dep on King -- Tim Booth Fri, 20 Feb 2015 14:18:45 +0000 qiime (1.8.0+dfsg-4) unstable; urgency=medium * d/copyright: Fix missing licenses Closes: #758026 -- Andreas Tille Wed, 13 Aug 2014 19:19:10 +0200 qiime (1.8.0+dfsg-3) unstable; urgency=medium * cme fix dpkg-control (remove useless Pre-Depends) * fixed watch file * king does not (Build-)Depend from libjogl-java any more Closes: #731190 * debian/patches/prevent_download_on_builds.patch: do not try to download uclust at package build time Closes: #754672 * emperor moved from Depends to Suggests since this depencency is not (yet) fullfilled in Debian. This might make some tests fail but for the moment there is no better chance to get qiime into the next release * debian/qiime.links: Remove hack to link to biom-format tools Closes: #742754 -- Andreas Tille Mon, 11 Aug 2014 15:57:14 +0200 qiime (1.8.0-1biolinux1) precise; urgency=low * Make QIIME report the Debian version, because the patches we add are significant. * New dep on Emperor * Add new deps on qcli and promote some recommends to dependencies based on http://qiime.org/install/install.html#manually-installing-qiime * Add little wrapper script to call parsinsert as ParsInsert * Pulled the adsense patch from Andreas. Noted these packages are totally out of sync. Oh well. * Dropped biom 1108 patch as this is in upstream * Added greengenes core data in /usr/share/qiime/data as this doesn't ever seem to change and other QIIME distributions include it. * Modified help text to reflect recent changes. * Patch on unit tests to overcome some problems running them * Remove denoiser symlink as there is no need for it now * Prevent attempts to download stuff (uclust, fasttree) during build * Added suggested dep on r-cran-optparse * More determined cleanup of temporary test data -- Tim Booth Mon, 10 Mar 2014 14:20:08 +0000 qiime (1.8.0+dfsg-2) unstable; urgency=medium * debian/qiime.links: Fix links to new biom_format * debian/control: - New dependency: python-qcli (this should be dropped in version 2.0 of qiime) - Recommends: python-mpi4py since this is used in some tests * debian/rules: Remove remainings from running test suite -- Andreas Tille Thu, 26 Dec 2013 07:39:57 +0100 qiime (1.8.0+dfsg-1) unstable; urgency=low * New upstream version * Fixed debian/watch * Suggests: torque-client Closes: #721902 * debian/control: - cme fix dpkg-control - rdp-classifier can only be suggested since it is not in Debian and currently it seems that it can only go into non-free - Canonical Vcs URLs * debian/patches/prevent_google_addsense.patch: Remove Google Addsense from user documentation to save user privacy -- Andreas Tille Sat, 21 Dec 2013 08:50:20 +0100 qiime (1.7.0-0biolinux2) precise; urgency=low * Added patch from https://github.com/qiime/qiime/pull/1108.patch so we can/must use biom-format 1.2.0 -- Tim Booth Wed, 29 Jan 2014 15:06:04 +0000 qiime (1.7.0+dfsg-1) unstable; urgency=low * Upload preparations done for BioLinux to Debian -- Andreas Tille Mon, 17 Jun 2013 18:28:26 +0200 qiime (1.7.0-0biolinux1) precise; urgency=low * New usptream * Adopt new naming convention for bl releases * Add usearch script to match uclust warning message * Re-fix biom-format script aliases (as links, needed for script to see them) * Clean out old patches * Patch to fix significant typo in error message * Patch to stop warning for matplotlib * Depend on newer Pynast (Pynast now maintained along with QIIME) -- Tim Booth Tue, 11 Jun 2013 16:49:19 +0100 qiime (1.6.0-0ubuntu2) precise; urgency=low * Add some aliases so that the python-biom-format tools can be called with .py extensions inside the qiime shell, because this is consistent with what QIIME users expect. -- Tim Booth Thu, 02 May 2013 15:05:34 +0100 qiime (1.6.0-0ubuntu1) precise; urgency=low * New upstream release * Don't bother re-packing the tarball for PPA. Package now builds the same with re-packed or pristine. * Remove t-test bug patch as this is in upstream * Re-jig RDP version patch which is simplified but still needed * Note the upstream no longer includes an example parameters.txt -- Tim Booth Fri, 04 Jan 2013 12:51:49 +0000 qiime (1.5.0+repack-2ubuntu11) precise; urgency=low [Tim Booth] * The support_files patch only solved part of the problem, so trying a different, and simpler, tack. * Changes from Debian: [Andreas Tille] * debian/rules: Use xz compression for binary packages -- Tim Booth Tue, 20 Nov 2012 12:26:24 +0000 qiime (1.5.0+dfsg-1) unstable; urgency=low * debian/copyright: - Add Files-Excluded to document what was removed from original source * debian/watch: Enable '+dfsg' / '+repack' suffix in Debian versions * debian/control: - Remove DM-Upload-Allowed - Standards-Version: 3.9.4 (no changes needed) - Priority: optional (per Debian Med policy) - normalised format - Build-Depends: ghc (instead of ghc6) Closes: #710774 -- Andreas Tille Wed, 29 Aug 2012 14:30:02 +0200 qiime (1.5.0+repack-2ubuntu10) precise; urgency=low * Made QIIME accept RDP classifier >2.2 though the patch is a total hack. Solves issue reported by MJC. * Add patch to make QIIME look in the Debian standard location for king.jar and other support_files * Added patch to fix alpha diversity bug and tested by running test_compare_alpha_diversities.py * QIIME now needs python-cogent 1.5.3 -- Tim Booth Wed, 14 Nov 2012 09:59:24 +0000 qiime (1.5.0+repack-2ubuntu5) precise; urgency=low * Tweaked startup script to report the QIIME version -- Tim Booth Thu, 11 Oct 2012 13:49:35 +0100 qiime (1.5.0+repack-2ubuntu4) precise; urgency=low * Remove python26_trim_sff_primers.patch as Qiime now requires 2.7 anyway * Avoid calling dh_auto_clean at all as it triggers a partial rebuild * Added various support files in /usr/share/qiime/support_files * Added various symlinks as Qiime wants everything in one place * Set python-biom-format as a hard dependency because even built-in self-test won't start without it * Added patch to self-test where it looks for default config file * Modified to work with new RDP-classifier package -- Tim Booth Tue, 14 Aug 2012 17:53:13 +0100 qiime (1.5.0-2) unstable; urgency=low * debian/control: - Recommends: python-biom-format Closes: #682199 - Depends: python >= 2.7 Closes: #682198 * debian/get-orig-source: For next release use xz compression of repackaged source * debian/rules: use xz compression -- Andreas Tille Mon, 06 Aug 2012 09:22:42 +0200 qiime (1.5.0-1) unstable; urgency=low * New upstream version (adapted patches + remove patch that was applied upstream) * debian/get-orig-source: Strip *.jar file from upstream source which should never have been there * debian/upstream: - more complete authors information in BibTeX conform format - Moved DOI+PMID to References * debian/qiime.links: Link to king.jar * debian/control: Depends: king * debhelper 9 (control+compat) -- Andreas Tille Tue, 08 May 2012 18:07:56 +0200 qiime (1.4.0-2) unstable; urgency=low * debian/qiime.install: Include *.py files Closes: #668999 -- Andreas Tille Mon, 16 Apr 2012 15:39:02 +0200 qiime (1.4.0-1) unstable; urgency=low * New upstream version (updated patches) * debian/patches/fix_shebang_lines.patch: Removed because file to patch was removed upstream * debian/copyright: rewritten to confirm DEP5 and verified using cme fix dpkg-copyright -- Andreas Tille Tue, 20 Mar 2012 14:41:20 +0100 qiime (1.3.0-3) unstable; urgency=low [ Charles Plessy ] * renamed debian/upstream-metadata.yaml to debian/upstream [ Andreas Tille ] * Standards-Version: 3.9.3 (no changes needed) * debian/patches/ghc_7.4.2_compatibility.patch: Fix build problem based on illegal use of 'import System' (Thanks to Joachim Breitner ) for the patch Closes: #663889 -- Andreas Tille Sat, 17 Mar 2012 19:19:38 +0100 qiime (1.3.0-2) unstable; urgency=low * debian/control: - Added myself to uploaders - moved from contrib/science to science because there are no non-free components used any more - Removed duplicated entry ${misc:Depends} - Extra package qiime-doc arch all to avoid - Provides/Replaces/Conflicts denoiser - Fix Vcs fields - DM-Upload-Allowed: yes - Build-Depends: + python-all-dev (>= 2.6) (instead of python-central) + python-sphinx to create python documentation * debian/rules: - short dh notation instead of cdbs Closes: #639389 - allow overriding python2 by environemnt which helps backporters like Tim for BioLinux - use calculated $(pkg) variable instead of fixed string 'qiime' * debian/{rules,qiime.install}: Adapted to new binary package layout * debian/qiime.{doc,links}: Move documentation into place and use packaged JavaScript libraries * debian/qiime-doc.doc-base * debian/upstream-metadata.yaml -- Andreas Tille Tue, 29 Nov 2011 09:23:18 +0100 qiime (1.3.0-0ubuntu6) lucid; urgency=low * Attempt to fix some errors reported by print_qiime_config -t Fixes to environment, configuration and small patches -- Tim Booth Wed, 02 Nov 2011 18:06:37 +0000 qiime (1.3.0-1) unstable; urgency=low * Bringing qiime to Debian [Steffen] * Some reformatting of debian/control -- Tim Booth Fri, 26 Aug 2011 17:48:30 +0200 qiime (1.3.0-0ubuntu5) lucid; urgency=low * Very minor fix to scripts/shell/qiime_environment -- Tim Booth Tue, 16 Aug 2011 12:35:06 +0100 qiime (1.3.0-0ubuntu4) lucid; urgency=low * New upstream release. Needs newer Python-Cogent and includes built-in denoiser, so I have now aliased denoiser to run the qiime wrapper. * As the upstream now contains a tiny compiled package I've had to make it arch dependent (support_files/denoiser/FlowgramAlignment code written in Haskell). * Added build dep on ghc6 for the same reson -- Tim Booth Tue, 19 Jul 2011 17:38:28 +0100 qiime (1.2.1-ubuntu5) lucid; urgency=low * Fixed silly error in qiime wrapper script * Added uclust wrapper to deal with uclust being expected but missing -- Tim Booth Thu, 24 Mar 2011 16:52:43 +0000 qiime (1.2.1-ubuntu4) lucid; urgency=low * Fixed dependency - needs python-cogent >= 1.5 -- Tim Booth Thu, 24 Mar 2011 15:33:03 +0000 qiime (1.2.1-ubuntu3) lucid; urgency=low * Moved .py scripts out of /usr/bin * Added /usr/bin/qiime wrapper script as per Bio-Linux * Added default configuration file * Cleaned up documentation * Added many dependencies (some of which are still not packaged) -- Tim Booth Thu, 24 Mar 2011 11:35:58 +0000 qiime (1.2.1-ubuntu2) lucid; urgency=low * Pulled 1.2.1 source and tried a rebuild. * Fixed Lintian changelog warning. -- Tim Booth Tue, 22 Mar 2011 13:55:49 +0000 qiime (1.2.1-2) experimental; urgency=low * Initial release (Closes: #587275) * Fixed Python 2.6 incompatibility. -- Steffen Moeller Wed, 02 Mar 2011 22:33:45 +0100 qiime (1.2.1-1) experimental; urgency=low * Corrected home page * Updated policy to 3.9.1 * Updated debian/README.Debian -- Steffen Moeller Wed, 02 Mar 2011 18:19:39 +0100 qiime (1.1.0-1) experimental; urgency=low * Initial release. -- Sri Girish Srinivasa Murthy Tue, 20 Jul 2010 00:03:02 +0200