compmetagen/micca repository overview

⁠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)
• 1.7.0: micca 1.7.0 (RDP Classifier release 2.12 included)
• 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