Mercurial > repos > geert-vandeweyer > mutect_wrapper

view readme.rst @ 5:f9a746877f6c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author geert-vandeweyer
date Thu, 13 Feb 2014 09:27:26 -0500
parents
children 3b2782fc9610
line wrap: on
line source

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.