Mercurial > repos > jjohnson > snpeff_with_dep
diff README @ 22:4430626bd994
Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 17 Jan 2013 13:00:52 -0600 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Thu Jan 17 13:00:52 2013 -0600 @@ -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/ +