Mercurial > repos > fubar > snpeff_3_3_wrapper

view snpeff_3_3/README @ 0:80e2dbf1b1f5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author fubar
date Sun, 11 Aug 2013 08:15:14 -0400
parents
children
line wrap: on
line source

Original from Jim Johnson:

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/

Updated to use JJs 3.3 repo and renamed by ross lazarus august 11 2013 for a 3.3 solution