Mercurial > repos > fubar > snpeff_3_3_wrapper
diff snpeff33/README @ 1:a1e35baae42a draft
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| author | fubar |
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| date | Mon, 30 Sep 2013 00:59:41 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpeff33/README Mon Sep 30 00:59:41 2013 -0400 @@ -0,0 +1,18 @@ +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