Mercurial > repos > jjohnson > snpeff_with_dep
comparison 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> |
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| date | Thu, 17 Jan 2013 13:00:52 -0600 |
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| 21:077c84a53846 | 22:4430626bd994 |
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| 1 These are galaxy tools for Snp Effect ( http://snpeff.sourceforge.net/ ) | |
| 2 The genome reference options used by the tools: | |
| 3 "SnpEff" snpEff.xml | |
| 4 "SnpEff Download" snpEff_download.xml | |
| 5 are taken from: tool-data/snpeffect_genomedb.loc | |
| 6 | |
| 7 The tool-data/snpeffect_genomedb.loc.sample file has the genomes references from the SnpEffect dwnloads page: | |
| 8 http://snpeff.sourceforge.net/download.html | |
| 9 The values for snpeffect_genomedb.loc.sample were populated by: | |
| 10 java -jar snpEff.jar cfg2table galaxy | grep 'option' | sed 's/^.*value="\([^"]*\)">\([^<]*\).*$/\1#\2/' | tr '#' '\t' >> snpeffect_genomedb.loc.sample | |
| 11 | |
| 12 This repository contains a tool_dependencies.xml file that will allow SnpEff and SnpSift to be automatically installed. | |
| 13 This will use the default location for genome reference downloads from the snpEff.config: | |
| 14 data_dir = ~/snpEff/data/ | |
| 15 |