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1 Original from Jim Johnson:
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2
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3 These are galaxy tools for Snp Effect ( http://snpeff.sourceforge.net/ )
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4 The genome reference options used by the tools:
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5 "SnpEff" snpEff.xml
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6 "SnpEff Download" snpEff_download.xml
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7 are taken from: tool-data/snpeffect_genomedb.loc
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8
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9 The tool-data/snpeffect_genomedb.loc.sample file has the genomes references from the SnpEffect dwnloads page:
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10 http://snpeff.sourceforge.net/download.html
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11 The values for snpeffect_genomedb.loc.sample were populated by:
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12 java -jar snpEff.jar cfg2table galaxy | grep 'option' | sed 's/^.*value="\([^"]*\)">\([^<]*\).*$/\1#\2/' | tr '#' '\t' >> snpeffect_genomedb.loc.sample
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13
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14 This repository contains a tool_dependencies.xml file that will allow SnpEff and SnpSift to be automatically installed.
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15 This will use the default location for genome reference downloads from the snpEff.config:
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16 data_dir = ~/snpEff/data/
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17
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18 Updated to use JJs 3.3 repo and renamed by ross lazarus august 11 2013 for a 3.3 solution
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