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Update tool_dependencies.xml for package_snpeff_3_3
author Jim Johnson <jj@umn.edu>
date Fri, 04 Oct 2013 09:31:27 -0500
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1 These are galaxy tools for SnpEff ( http://snpeff.sourceforge.net/ )
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3 This repository contains a tool_dependencies.xml file that will attempt to automatically install SnpEff and SnpSift.
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5 This will use the default location for genome reference downloads from the snpEff.config:
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6 data_dir = ~/snpEff/data/
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7 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.
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9 The genome reference options used by the tools:
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10 "SnpEff" snpEff.xml
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11 "SnpEff Download" snpEff_download.xml
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12 are taken from: tool-data/snpeffect_genomedb.loc
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14 There are 2 datamanagers to download and install prebuilt SnpEff Genome databases:
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15 data_manager_snpeff_databases - generates a list of available SnpEff genome databases into the tool-data/snpeff_databases.loc
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16 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
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