qiime 1.8.0+dfsg-2 source package in Ubuntu


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 <email address hidden>  Thu, 26 Dec 2013 07:39:57 +0100

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Uploaded by:
Debian Med on 2013-12-30
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Original maintainer:
Debian Med
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Medium Urgency

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Series Pocket Published Component Section
Trusty release on 2013-12-30 universe science


File Size SHA-256 Checksum
qiime_1.8.0+dfsg-2.dsc 1.5 KiB cf6e5ee248c27bb92a5aa4ff459aadfd9b29035f93b0381dd461eb33a29b4a26
qiime_1.8.0+dfsg.orig.tar.xz 14.0 MiB cb9572d566a793ebaf47ecca4de0df895a991e97986594554cb927bb48d06a79
qiime_1.8.0+dfsg-2.debian.tar.gz 21.4 KiB 0f5b9479019dd985005ce8ac2ec30ab011bf3d74d60db415548b4de75922af0d

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Binary packages built by this source

qiime: 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.

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