Various Galaxy tools for running SNVMix and filtering/annotating the SNVMix output files

Installation
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1) Place these files in $GALAXY_HOME/tools and compile/install SNVMix2 if you haven't already done so (also copy/link the SNVMix2 binary, 
identify_nonsynonymous_mutations.pl and filter_snvmix.pl to /usr/local/bin or some other location in the default PATH, also ensure they are executable)
2) Modify your configuration files appropriately
-add the tools to $GALAXY_HOME/tool_conf.xml (under the NGS analysis section, create a "variant calling" section), see the tool_conf.xml.sample for an example
-create or modify $GALAXY_HOME/sam_fa_indices.loc to match the example provided (points galaxy to the fasta files containing the genome that was used during the alignment step).  These are needed by SNVMix.

Requirements
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1) SNP list (can be user-provided), an example for hg18 is provided at the FTP site below
2) Codon-lookup table (used for annotation), an example based on Ensembl 54 and hg18 is also provided at the FTP site provided

ftp://ftp03.bcgsc.ca/public/rmorin/resources/
(also see README.txt in that directory)

3) SNVMix binary version 0.12.* or later (source can be downloaded at the link provided)
-follow installation instructions and put SNVMix2 binary in a location on the galaxy user's PATH

http://compbio.bccrc.ca/?page_id=204

Contacts: 
Rodrigo Goya for problems with SNVMix2 binary
rgoya@bcgsc.ca

Ryan Morin for other problems
rmorin@bcgsc.ca