Mercurial > repos > geert-vandeweyer > mutect_wrapper

changeset 5:f9a746877f6c draft

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Uploaded
author geert-vandeweyer
date Thu, 13 Feb 2014 09:27:26 -0500
parents e774395351f5
children 61799c55d169
files readme.rst
diffstat 1 files changed, 20 insertions(+), 0 deletions(-) [+]
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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.
+
+