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Change tool dependency to package_snpeff_3_2, now uses environment variable: SNPEFF_JAR_PATH for the location of snpeff jar files.
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Jim Johnson <jj@umn.edu> |
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Wed, 18 Sep 2013 10:49:56 -0500 |
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c07c403fc470 |
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1 These are galaxy tools for Snp Effect ( http://snpeff.sourceforge.net/ )
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2 The genome reference options used by the tools:
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3 "SnpEff" snpEff.xml
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4 "SnpEff Download" snpEff_download.xml
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5 are taken from: tool-data/snpeffect_genomedb.loc
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7 The tool-data/snpeffect_genomedb.loc.sample file has the genomes references from the SnpEffect dwnloads page:
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8 http://snpeff.sourceforge.net/download.html
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9 The values for snpeffect_genomedb.loc.sample were populated by:
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10 java -jar snpEff.jar cfg2table galaxy | grep 'option' | sed 's/^.*value="\([^"]*\)">\([^<]*\).*$/\1#\2/' | tr '#' '\t' >> snpeffect_genomedb.loc.sample
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12 This repository contains a tool_dependencies.xml file that will allow SnpEff and SnpSift to be automatically installed.
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13 This will use the default location for genome reference downloads from the snpEff.config:
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14 data_dir = ~/snpEff/data/
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