Mercurial > repos > fubar > snpeff_3_3_wrapper

Original from Jim Johnson:

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/

Updated to use JJs 3.3 repo and renamed by ross lazarus august 11 2013 for a 3.3 solution
author	fubar
date	Mon, 30 Sep 2013 00:59:41 -0400
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