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Fixes. MuTect now works
author geert-vandeweyer
date Mon, 17 Feb 2014 11:54:09 -0500
parents 3b2782fc9610
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Galaxy wrapper for muTect
=========================

This wrapper is written by Geert Vandeweyer. MuTect is a software package developed at the 
Broad Institute to analyse next-generation resequencing data. 

The recommended installation is by means of the toolshed_.

.. _toolshed: http://toolshed.g2.bx.psu.edu/view/geert-vandeweyer/mutect_wrapper

Galaxy should be able to install samtools dependencies automatically
for you. muTect must be installed manually. After installation you need to edit the env.sh files that are installed together with the wrapper.

You must edit the MUTECT_PATH environment variable in the file:

<tool_dependency_dir>/environment_settings/MUTECT_PATH/geert-vandeweyer/mutect/<hash_string>/env.sh

to point to the folder where you have installed MUTECT.


Finally, you need to set up the <path>/galaxy-dist/tool-data/all.fasta file for the correct path of your reference genomes.