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diff README @ 0:e1d9f6a0ad53

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author jjohnson
date Thu, 04 Jul 2013 10:43:55 -0400
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children 6ad9205c1307
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Thu Jul 04 10:43:55 2013 -0400
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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/
+