diff README @ 2:6ad9205c1307

Update to SnpEff version 3.3

--- a/README	Thu Jul 04 09:49:15 2013 -0500
+++ b/README	Fri Oct 04 09:09:29 2013 -0500
@@ -1,15 +1,18 @@
-These are galaxy tools for Snp Effect ( http://snpeff.sourceforge.net/ )
+These are galaxy tools for SnpEff ( http://snpeff.sourceforge.net/ )
+
+This repository contains a tool_dependencies.xml file that will attempt to automatically install SnpEff and SnpSift.   
+
+This will use the default location for genome reference downloads from the snpEff.config:
+data_dir = ~/snpEff/data/
+You can manually edit the installed snpEff.config and change the location, or you can create a symbolic link to the desired data location from ~/snpEff.
+
 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
+There are 2 datamanagers to download and install prebuilt SnpEff Genome databases:
+  data_manager_snpeff_databases - generates a list of available SnpEff genome databases into the tool-data/snpeff_databases.loc 
+  data_manager_snpeff_download - downloads a SnpEff genome database selected from: tool-data/snpeff_databases.loc and adds entries to snpeff_genomedb.loc,snpeff_regulationdb.loc,snpeff_annotations.loc 
 
-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/