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Update for snpEff v3.2
author Jim Johnson <jj@umn.edu>
date Tue, 07 May 2013 14:58:15 -0500
parents 4430626bd994
children
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4430626bd994 Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
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1 These are galaxy tools for Snp Effect ( http://snpeff.sourceforge.net/ )
4430626bd994 Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
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2 The genome reference options used by the tools:
4430626bd994 Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
diff changeset
3 "SnpEff" snpEff.xml
4430626bd994 Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
diff changeset
4 "SnpEff Download" snpEff_download.xml
4430626bd994 Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
diff changeset
5 are taken from: tool-data/snpeffect_genomedb.loc
4430626bd994 Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
diff changeset
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4430626bd994 Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
diff changeset
7 The tool-data/snpeffect_genomedb.loc.sample file has the genomes references from the SnpEffect dwnloads page:
4430626bd994 Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
diff changeset
8 http://snpeff.sourceforge.net/download.html
4430626bd994 Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
diff changeset
9 The values for snpeffect_genomedb.loc.sample were populated by:
4430626bd994 Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
diff changeset
10 java -jar snpEff.jar cfg2table galaxy | grep 'option' | sed 's/^.*value="\([^"]*\)">\([^<]*\).*$/\1#\2/' | tr '#' '\t' >> snpeffect_genomedb.loc.sample
4430626bd994 Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
diff changeset
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4430626bd994 Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
diff changeset
12 This repository contains a tool_dependencies.xml file that will allow SnpEff and SnpSift to be automatically installed.
4430626bd994 Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
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13 This will use the default location for genome reference downloads from the snpEff.config:
4430626bd994 Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
diff changeset
14 data_dir = ~/snpEff/data/
4430626bd994 Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
diff changeset
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