Author: moeller Date: 2011-08-26 13:19:44 +0000 (Fri, 26 Aug 2011) New Revision: 7555
Modified: trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/control Log: Some formatting on the control file. Modified: trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/control =================================================================== --- trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/control 2011-08-26 13:01:08 UTC (rev 7554) +++ trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/control 2011-08-26 13:19:44 UTC (rev 7555) @@ -4,7 +4,7 @@ Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: Sri Girish Srinivasa Murthy <[email protected]>, Steffen Moeller <[email protected]>, Tim Booth <[email protected]> Build-Depends: debhelper (>= 8), cdbs, python, python-central, python-cogent ( >= 1.5.1 ), python-numpy, python-matplotlib, ghc6 -Standards-Version: 3.9.1 +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/ @@ -12,31 +12,39 @@ Package: qiime Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends}, python-pynast, python-cogent ( >= 1.5.1 ) +Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends}, python-pynast (>= 1.1)|pynast (>= 1.1), python-cogent ( >= 1.5.1 ) Recommends: blast2 | blast+-legacy, cd-hit, rdp-classifier, chimeraslayer, muscle, infernal, fasttree, ampliconnoise, python-matplotlib, python-numpy Conflicts: denoiser Replaces: denoiser +#Provides: denoiser # matter of discussion Suggests: t-coffee, cytoscape 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, + 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. + 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
