This is a new implementation of the mPuma pipeline (http://mpuma.sourceforge.net/) for the Galaxy platform (http://galaxyproject.org/). mPuma allows researchers to profile microbial communities using a de novo assembly approach to form Operational Taxonomic Units (OTUs). While originally designed to support the analysis of cpn60 based amplicons, mPUMA can be used to analyze data from any suitable DNA barcode.
The original mPuma pipeline was implemented as a standalone terminal program. For this new implementation it has been decomposed into a suite of independent tools: the mPuma pipeline is executed as a Galaxy workflow, making it easier to run, debug, and generally more usefull, since some of the tools are new and also subpipelines can be easilly configured.
The pipeline is already installed at PURL (See section Using mPuma-Galaxy bellow). You can also install the tool suite at your own Galaxy server (recommended) following the instructions of the section Installation bellow.
See wiki.
In order to install the tools of this suite, it is recommended to use the toolshed automated installation. You can also do it manually; stop Galaxy and either:
Unpack and execute deploy-mPuma-Galaxy.sh at your own risk. The script will copy the necessary files and edit tool-conf.xml. You need to edit the galaxy variable and add the path to your galaxy distribution.
Unpack and install manually (perform the steps that are automated by the above script). Copy the whole directory galaxy-dist/tools/mPuma/ to the tools directory on your Galaxy system. Same for test-data. Then edit tool-conf.xml to include the same content as galaxy-dist/tool_conf.xml, except the </toolbox> tag. This way you can add the mPuma tool suite wherever you like on the Galaxy left column.
Start Galaxy.
The Galaxy page (PURL) contains a workflow and history representing the mPuma pipeline, using a test dataset from the original publication. The pipeline can be run by importing both the history and the workflow and executing the workflow with the datasets from the history (We recommend doing this in your own Galaxy server).
Mikel Egaña Aranguren is funded by the Marie Curie Cofund programme (FP7) of the European Union through the UPM (Spain) and the Genomic Resources Group (http://www.genomic-resources.eu/) of the University of Basque Country (UPV/EHU).