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Last pushed: 7 months ago
Short Description
micca - MICrobial Community Analysis
Full Description

micca - Docker

micca (MICrobial Community Analysis) is a software pipeline for the processing
of amplicon sequencing data, from raw sequences to OTU tables, taxonomy
classification and phylogenetic tree inference. The pipeline can be applied to a
range of highly conserved genes/spacers, such as 16S rRNA gene, Internal
Transcribed Spacer (ITS) and 28S rRNA. Homepage: http://www.micca.org.

The RDP classifier is preinstalled in the Docker image, so you can check the
software version by typing echo $RDPPATH
(see https://hub.docker.com/r/compmetagen/rdpclassifier/).

Available Tags/Versions

  • latest: GitHub snapshot (master)
  • 1.6.2: micca 1.6.2 (RDP Classifier release 2.11 included)
  • 1.6.1: micca 1.6.1 (RDP Classifier release 2.11 included)
  • 1.6.0: micca 1.6.0 (RDP Classifier release 2.11 included)
  • 1.5.0: micca 1.5.0 (RDP Classifier release 2.11 included)
  • 1.4.0: micca 1.4.0 (RDP Classifier release 2.11 included)
  • 1.3.0: micca 1.3.0 (RDP Classifier release 2.11 included)
  • 1.2.2: micca 1.2.2 (RDP Classifier release 2.11 included)

Quickstart

  1. Download the latest version:

    docker pull compmetagen/micca

  2. Run an instance of the image, mounting the host working directory
    (e.g. /Users/davide/micca) on to the container working directory
    /micca:

    docker run --rm -t -i -v /Users/davide/micca:/micca -w /micca compmetagen/micca /bin/bash

    You need to write something like -v //c/Users/davide/micca:/micca if
    you are in Windows or -v /home/davide/micca:/micca in Linux. The
    --rm option automatically removes the container when it exits.

  3. Run micca without parameters:

    root@68f6784e1101:/micca# micca

Docker Pull Command
Owner
compmetagen
Source Repository

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