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author ryanmorin
date Tue, 18 Oct 2011 18:32:07 -0400
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1 Various Galaxy tools for running SNVMix and filtering/annotating the SNVMix output files 1 Various Galaxy tools for running SNVMix and filtering/annotating the SNVMix output files
2 2
3 Installation 3 Installation
4 ------------ 4 ------------
5 5
6 1) Place these files in $GALAXY_HOME/tools 6 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,
7 2) Modify your configuration files appropriately, for example, add the tools to $GALAXY_HOME/tool_conf.xml (under the NGS analysis section, create a "variant calling" section) 7 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)
8 2) Modify your configuration files appropriately
9 -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
10 -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.
8 11
9 Requirements 12 Requirements
10 ------------ 13 ------------
11 1) SNP list (can be user-provided), an example for hg18 is provided at the FTP site below 14 1) SNP list (can be user-provided), an example for hg18 is provided at the FTP site below
12 2) Codon-lookup table (used for annotation), an example based on Ensembl 54 and hg18 is also provided at the FTP site provided 15 2) Codon-lookup table (used for annotation), an example based on Ensembl 54 and hg18 is also provided at the FTP site provided