Mercurial > repos > jjohnson > snpeff

view README @ 4:47ddc9f4d0b6

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Add tests to datamanagers
author Jim Johnson <jj@umn.edu>
date Mon, 07 Oct 2013 10:59:44 -0500
parents 6ad9205c1307
children 8952990fcab9
line wrap: on
line source

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

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