|
0
|
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
|
