Source: qiime
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>,
           Tim Booth <tbooth@ceh.ac.uk>,
           Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
               python-all-dev (>= 2.7),
               python-cogent (>= 1.5.3),
               python-numpy,
               python-matplotlib,
               ghc,
               python-sphinx
Standards-Version: 3.9.5
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/qiime/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/qiime/trunk/
Homepage: http://www.qiime.org/
X-Python-Version: >= 2.7

Package: qiime
Architecture: any
Depends: ${shlibs:Depends},
         ${misc:Depends},
         ${python:Depends},
         pynast (>= 1.2),
         python-cogent (>= 1.5.3),
         king,
         python-biom-format,
         python-qcli
Recommends: blast2 | blast+-legacy,
            cd-hit,
            chimeraslayer,
            muscle,
            infernal,
            fasttree,
            ampliconnoise,
            python-matplotlib,
            python-numpy,
            python-mpi4py,
            libjs-jquery
Suggests: t-coffee,
          cytoscape,
          rdp-classifier,
          torque-client
Conflicts: denoiser
Provides: denoiser
Replaces: denoiser
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.

Package: qiime-doc
Architecture: all
Section: doc
Depends: ${misc:Depends},
         libjs-jquery,
         libjs-underscore
Description: Quantitative Insights Into Microbial Ecology (tutorial)
 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.
 .
 This package contains the documentation and a tutorial.
