Mercurial > repos > jjohnson > snpeff
diff README @ 0:c07c403fc470
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| author | jjohnson |
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| date | Thu, 17 Jan 2013 16:31:12 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Thu Jan 17 16:31:12 2013 -0500 @@ -0,0 +1,15 @@ +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/ +