Author: moeller Date: 2010-06-26 23:29:28 +0000 (Sat, 26 Jun 2010) New Revision: 4949
Added: trunk/packages/qiime/ trunk/packages/qiime/trunk/ trunk/packages/qiime/trunk/debian/ trunk/packages/qiime/trunk/debian/README.Debian trunk/packages/qiime/trunk/debian/changelog trunk/packages/qiime/trunk/debian/control trunk/packages/qiime/trunk/debian/copyright trunk/packages/qiime/trunk/debian/docs trunk/packages/qiime/trunk/debian/pyversions trunk/packages/qiime/trunk/debian/rules trunk/packages/qiime/trunk/debian/source/ trunk/packages/qiime/trunk/debian/source/format trunk/packages/qiime/trunk/debian/watch Log: Rudimentary packaging attempt Property changes on: trunk/packages/qiime/trunk/debian ___________________________________________________________________ Added: mergeWithUpstream + 1 Added: trunk/packages/qiime/trunk/debian/README.Debian =================================================================== --- trunk/packages/qiime/trunk/debian/README.Debian (rev 0) +++ trunk/packages/qiime/trunk/debian/README.Debian 2010-06-26 23:29:28 UTC (rev 4949) @@ -0,0 +1,8 @@ +QIIME for Debian +================ + +QIIME is a very powerful environment, but the core of its power +stems from the tools underneath. + +Not all those tools that QIIME can work with are yet available +with Debian. If you find resources to help - please do. Added: trunk/packages/qiime/trunk/debian/changelog =================================================================== --- trunk/packages/qiime/trunk/debian/changelog (rev 0) +++ trunk/packages/qiime/trunk/debian/changelog 2010-06-26 23:29:28 UTC (rev 4949) @@ -0,0 +1,6 @@ +qiime (1.1.0-1) unstable; urgency=low + + * Initial release (Closes: #587275) + + -- Sri Girish Srinivasa Murthy <[email protected]> Sun, 27 Jun 2010 01:00:47 +0200 + Added: trunk/packages/qiime/trunk/debian/control =================================================================== --- trunk/packages/qiime/trunk/debian/control (rev 0) +++ trunk/packages/qiime/trunk/debian/control 2010-06-26 23:29:28 UTC (rev 4949) @@ -0,0 +1,42 @@ +Source: qiime +Section: python +Priority: extra +Maintainer: Sri Girish Srinivasa Murthy <[email protected]> +Uploaders: Steffen Moeller <[email protected]> +Build-Depends: debhelper (>= 7), cdbs, python, python-central, python-cogent, python-numpy, python-matplotlib +Standards-Version: 3.8.4 +Homepage: http://pynast.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/ + +Package: qiime +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends} +Recommends: blast2 +Suggests: muscle, infernal, t-coffee +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. Added: trunk/packages/qiime/trunk/debian/copyright =================================================================== --- trunk/packages/qiime/trunk/debian/copyright (rev 0) +++ trunk/packages/qiime/trunk/debian/copyright 2010-06-26 23:29:28 UTC (rev 4949) @@ -0,0 +1,28 @@ +This work was packaged for Debian by: + + Sri Girish Srinivasa Murthy <[email protected]> + and Steffen Moeller <[email protected]> + on Fri, 25 Jun 2010 17:23:58 +0200 + +It was downloaded from <http://pynast.sorceforge.net> + +Upstream Author: + + Greg Caporaso <[email protected]> + Kyle Bittinger + +Copyright: + + Copyright 2010, The QIIME Project + +License: + + GPL-2 + +The Debian packaging is: + + Copyright (C) 2010 Sri Girish Srinivasa Murthy <[email protected]> + and Steffen Moeller <[email protected]> + +and is licensed under the same copyright, +see `/usr/share/common-licenses/GPL-2'. Added: trunk/packages/qiime/trunk/debian/docs =================================================================== --- trunk/packages/qiime/trunk/debian/docs (rev 0) +++ trunk/packages/qiime/trunk/debian/docs 2010-06-26 23:29:28 UTC (rev 4949) @@ -0,0 +1,5 @@ +README +ChangeLog +qiime_parameters.txt +qiime_tutorial/ +doc/* Added: trunk/packages/qiime/trunk/debian/pyversions =================================================================== --- trunk/packages/qiime/trunk/debian/pyversions (rev 0) +++ trunk/packages/qiime/trunk/debian/pyversions 2010-06-26 23:29:28 UTC (rev 4949) @@ -0,0 +1 @@ +2.6 Added: trunk/packages/qiime/trunk/debian/rules =================================================================== --- trunk/packages/qiime/trunk/debian/rules (rev 0) +++ trunk/packages/qiime/trunk/debian/rules 2010-06-26 23:29:28 UTC (rev 4949) @@ -0,0 +1,13 @@ +#!/usr/bin/make -f +# -*- makefile -*- + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +export DEB_PYTHON_SYSTEM=pycentral + +include /usr/share/cdbs/1/rules/debhelper.mk +include /usr/share/cdbs/1/class/python-distutils.mk + +clean:: + rm -rf build build-stamp Property changes on: trunk/packages/qiime/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/qiime/trunk/debian/source/format =================================================================== --- trunk/packages/qiime/trunk/debian/source/format (rev 0) +++ trunk/packages/qiime/trunk/debian/source/format 2010-06-26 23:29:28 UTC (rev 4949) @@ -0,0 +1 @@ +3.0 (quilt) Added: trunk/packages/qiime/trunk/debian/watch =================================================================== --- trunk/packages/qiime/trunk/debian/watch (rev 0) +++ trunk/packages/qiime/trunk/debian/watch 2010-06-26 23:29:28 UTC (rev 4949) @@ -0,0 +1,2 @@ +version=3 +http://sf.net/pynast/PyNAST-([.0-9]+)\.tgz _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
