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Fix issues with snpEff commandline template and add test cases
author Jim Johnson <jj@umn.edu>
date Thu, 28 Mar 2013 12:29:45 -0500
parents c07c403fc470
children
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These are galaxy tools for Snp Effect ( http://snpeff.sourceforge.net/ )
The genome reference options used by the tools:
    "SnpEff"  snpEff.xml
    "SnpEff Download" snpEff_download.xml
are taken from: tool-data/snpeffect_genomedb.loc

The tool-data/snpeffect_genomedb.loc.sample file has the genomes references from the SnpEffect dwnloads page:
http://snpeff.sourceforge.net/download.html
The values for snpeffect_genomedb.loc.sample were populated by:
java -jar snpEff.jar cfg2table galaxy | grep 'option' | sed 's/^.*value="\([^"]*\)">\([^<]*\).*$/\1#\2/' | tr '#' '\t' >> snpeffect_genomedb.loc.sample

This repository contains a tool_dependencies.xml file that will allow SnpEff and SnpSift to be automatically installed.   
This will use the default location for genome reference downloads from the snpEff.config:
data_dir = ~/snpEff/data/