Author: tille Date: 2011-08-29 06:54:01 +0000 (Mon, 29 Aug 2011) New Revision: 7573
Added: trunk/packages/qiime/trunk/ trunk/packages/qiime/trunk/debian/changelog trunk/packages/qiime/trunk/debian/control Removed: trunk/packages/qiime/trunk/debian/changelog trunk/packages/qiime/trunk/debian/conffiles trunk/packages/qiime/trunk/debian/control Modified: trunk/packages/qiime/trunk/debian/README.Debian Log: Move from contrib to main; hopefully better up to date and better understandable README.Debian Modified: trunk/packages/qiime/trunk/debian/README.Debian =================================================================== --- trunk/packages/qiime/trunk_debhelper/debian/README.Debian 2011-08-28 22:45:23 UTC (rev 7570) +++ trunk/packages/qiime/trunk/debian/README.Debian 2011-08-29 06:54:01 UTC (rev 7573) @@ -18,28 +18,9 @@ first to profit from now joint forces on getting the packages to a best-possible shape for everyone. -The distribution is set to contrib because of - * the strong recommends to use uclust that is not shipped with - Debian as a binary only package. - * python-cogent is a dependency that is non-free - - -Disambiguation of versions in bio-linux, Debian and Ubuntu ----------------------------------------------------------- - -The conflict reports in the control file is originally indiciated against -bio-linux-qiime (<= bl1.1.x). The prefix "bl" is unfortunate since the -Debian packaging tools demand (and the Debian policy) demand the version -to start with a number, not a character. The version is now removed from -that indicated conflict. - -Depending on who was performing the last editing of the package, versions -are either specified with a suffix "-N", N numeric, for uploads to Debian, -or with the suffix "-ubuntuN". The changelog shall show the Ns to increase -and be reset for new upstream versions. This is yet slightly different -from the common practice to have the Ubuntu vesion keep the last Debian -version (or start a new one as 0) and have the version extended to -"NubuntuM" with M reset to 1 with every new Debian version. Either way -makes sense. The current approach indiciates better that some upload -to Debian may not yet have happened. - +Qiime wants very much to use the UClust binary, but this is not free software. +However, it is available right now free-of-charge if: + a) You are an academic user and only want the 32-bit version. + b) You promise to use the UClust application only as part of Qiime. +You can download uclust from + http://www.drive5.com/uclust/downloads1_2_21q.html Deleted: trunk/packages/qiime/trunk/debian/changelog =================================================================== --- trunk/packages/qiime/trunk_debhelper/debian/changelog 2011-08-28 22:45:23 UTC (rev 7570) +++ trunk/packages/qiime/trunk/debian/changelog 2011-08-29 06:54:01 UTC (rev 7573) @@ -1,78 +0,0 @@ -qiime (1.3.0-1) UNRELEASED; urgency=low - - * New upstream version - * debian/control: - - Added myself to uploaders - - needs higher version of python-cogent - [Steffen, Tim] - * Escaping from experimental since pynast has escaped it. - - -- Andreas Tille <[email protected]> Wed, 03 Aug 2011 10:59:42 +0200 - -qiime (1.2.1-6) experimental; urgency=low - - [Andreas Tille] - * Dropped cdbs in favour of dh - * Debhelper 8 (compat+control) - * Use debian/{install,dirs) to enable better readable debian/rules - * debian/rules: - - override_dh_compress - - override_dh_installchangelogs - - [Steffen Moeller] - * Updates to debian/README.Debian - * Policy updated to 3.9.2 - - -- Steffen Moeller <[email protected]> Fri, 29 Apr 2011 22:56:37 +0200 - -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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Wed, 02 Mar 2011 18:19:39 +0100 - -qiime (1.1.0-1) experimental; urgency=low - - * Initial release. - - -- Sri Girish Srinivasa Murthy <[email protected]> Tue, 20 Jul 2010 00:03:02 +0200 - Copied: trunk/packages/qiime/trunk/debian/changelog (from rev 7571, trunk/packages/qiime/trunk_debhelper/debian/changelog) =================================================================== --- trunk/packages/qiime/trunk/debian/changelog (rev 0) +++ trunk/packages/qiime/trunk/debian/changelog 2011-08-29 06:54:01 UTC (rev 7573) @@ -0,0 +1,92 @@ +qiime (1.3.0-1) UNRELEASED; urgency=low + + [Andreas Tille] + * New upstream version + * debian/control: + - Added myself to uploaders + - needs higher version of python-cogent + - moved from contrib/science to science because there are + no non-free components used any more + * Removed denoiser from Recommends because it is included + in the package itself + * Removed empty file debian/conffiles + * debian/README.Debian: + - Removed non-free remark about cogent + - Added remark about uclust + - Removed explanation of version numbers refering to BioLinux. + The remark was hard to understand either for Debian or Ubuntu + users because they do not see in their packages what is + described inside README.Debian. + + [Steffen Möller, Tim Booth] + * Escaping from experimental since pynast has escaped it. + + -- Andreas Tille <[email protected]> Wed, 03 Aug 2011 10:59:42 +0200 + +qiime (1.2.1-6) experimental; urgency=low + + [Andreas Tille] + * Dropped cdbs in favour of dh + * Debhelper 8 (compat+control) + * Use debian/{install,dirs) to enable better readable debian/rules + * debian/rules: + - override_dh_compress + - override_dh_installchangelogs + + [Steffen Moeller] + * Updates to debian/README.Debian + * Policy updated to 3.9.2 + + -- Steffen Moeller <[email protected]> Fri, 29 Apr 2011 22:56:37 +0200 + +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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Wed, 02 Mar 2011 18:19:39 +0100 + +qiime (1.1.0-1) experimental; urgency=low + + * Initial release. + + -- Sri Girish Srinivasa Murthy <[email protected]> Tue, 20 Jul 2010 00:03:02 +0200 + Deleted: trunk/packages/qiime/trunk/debian/conffiles =================================================================== Deleted: trunk/packages/qiime/trunk/debian/control =================================================================== --- trunk/packages/qiime/trunk_debhelper/debian/control 2011-08-28 22:45:23 UTC (rev 7570) +++ trunk/packages/qiime/trunk/debian/control 2011-08-29 06:54:01 UTC (rev 7573) @@ -1,54 +0,0 @@ -Source: qiime -Section: contrib/science -Priority: extra -Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Steffen Moeller <[email protected]>, - Tim Booth <[email protected]>, - Andreas Tille <[email protected]> -Build-Depends: debhelper (>= 8), python, python-central, python-cogent, python-numpy, python-matplotlib -Standards-Version: 3.9.2 -Homepage: http://qiime.sourceforge.net/ -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/qiime/trunk/?rev=0&sc=0 -Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/qiime/trunk/ -XS-Python-Version: >= 2.5 - -Package: qiime -Architecture: all -Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends}, python-pynast, python-cogent ( >= 1.5.1 ) -Recommends: blast2, cd-hit, denoiser, rdp-classifier, chimeraslayer, muscle, infernal, fasttree -Suggests: t-coffee, cytoscape -Conflicts: bio-linux-qiime -XB-Python-Version: ${python:Versions} -Description: Quantitative Insights Into Microbial Ecology - QIIME (canonically pronounced ‘Chime’) is a pipeline for performing - microbial community analysis that integrates many third party tools which - have become standard in the field. A standard QIIME analysis begins with - sequence data from one or more sequencing platforms, including - * Sanger, - * Roche/454, and - * Illumina GAIIx. - With all the underlying tools installed, - of which not all are yet available in Debian (or any other Linux - distribution), QIIME can perform - * library de-multiplexing and quality filtering; - * denoising with PyroNoise; - * OTU and representative set picking with uclust, cdhit, mothur, BLAST, or other tools; - * taxonomy assignment with BLAST or the RDP classifier; - * sequence alignment with PyNAST, muscle, infernal, or other tools; - * phylogeny reconstruction with FastTree, raxml, clearcut, or other tools; - * alpha diversity and rarefaction, including visualization of results, - using over 20 metrics including Phylogenetic Diversity, chao1, and - observed species; - * beta diversity and rarefaction, including visualization of results, - using over 25 metrics including weighted and unweighted UniFrac, - Euclidean distance, and Bray-Curtis; - * summarization and visualization of taxonomic composition of samples - using pie charts and histograms - and many other features. - . - QIIME includes parallelization capabilities for many of the - computationally intensive steps. By default, these are configured to - utilize a mutli-core environment, and are easily configured to run in - a cluster environment. QIIME is built in Python using the open-source - PyCogent toolkit. It makes extensive use of unit tests, and is highly - modular to facilitate custom analyses. Copied: trunk/packages/qiime/trunk/debian/control (from rev 7571, trunk/packages/qiime/trunk_debhelper/debian/control) =================================================================== --- trunk/packages/qiime/trunk/debian/control (rev 0) +++ trunk/packages/qiime/trunk/debian/control 2011-08-29 06:54:01 UTC (rev 7573) @@ -0,0 +1,54 @@ +Source: qiime +Section: science +Priority: extra +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Steffen Moeller <[email protected]>, + Tim Booth <[email protected]>, + Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 8), python, python-central, python-cogent, python-numpy, python-matplotlib +Standards-Version: 3.9.2 +Homepage: http://qiime.sourceforge.net/ +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/qiime/trunk/?rev=0&sc=0 +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/qiime/trunk/ +XS-Python-Version: >= 2.5 + +Package: qiime +Architecture: all +Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends}, python-pynast, python-cogent ( >= 1.5.1 ) +Recommends: blast2, cd-hit, rdp-classifier, chimeraslayer, muscle, infernal, fasttree +Suggests: t-coffee, cytoscape +Conflicts: bio-linux-qiime +XB-Python-Version: ${python:Versions} +Description: Quantitative Insights Into Microbial Ecology + QIIME (canonically pronounced ‘Chime’) is a pipeline for performing + microbial community analysis that integrates many third party tools which + have become standard in the field. A standard QIIME analysis begins with + sequence data from one or more sequencing platforms, including + * Sanger, + * Roche/454, and + * Illumina GAIIx. + With all the underlying tools installed, + of which not all are yet available in Debian (or any other Linux + distribution), QIIME can perform + * library de-multiplexing and quality filtering; + * denoising with PyroNoise; + * OTU and representative set picking with uclust, cdhit, mothur, BLAST, or other tools; + * taxonomy assignment with BLAST or the RDP classifier; + * sequence alignment with PyNAST, muscle, infernal, or other tools; + * phylogeny reconstruction with FastTree, raxml, clearcut, or other tools; + * alpha diversity and rarefaction, including visualization of results, + using over 20 metrics including Phylogenetic Diversity, chao1, and + observed species; + * beta diversity and rarefaction, including visualization of results, + using over 25 metrics including weighted and unweighted UniFrac, + Euclidean distance, and Bray-Curtis; + * summarization and visualization of taxonomic composition of samples + using pie charts and histograms + and many other features. + . + QIIME includes parallelization capabilities for many of the + computationally intensive steps. By default, these are configured to + utilize a mutli-core environment, and are easily configured to run in + a cluster environment. QIIME is built in Python using the open-source + PyCogent toolkit. It makes extensive use of unit tests, and is highly + modular to facilitate custom analyses. _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
