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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="snpEff" version="4.0">
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4 <install version="1.0">
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5 <actions>
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6 <action type="download_by_url">https://downloads.sourceforge.net/project/snpeff/snpEff_v4_0_core.zip</action>
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7 <action type="move_directory_files">
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8 <source_directory>.</source_directory>
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9 <destination_directory>$INSTALL_DIR</destination_directory>
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10 </action>
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11 <action type="shell_command">sed -i.orig -e 's;http://downloads.sourceforge.net/project/snpeff/databases;https://snpeff-data.galaxyproject.org/databases;g' $INSTALL_DIR/snpEff.config</action>
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12 <action type="set_environment">
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13 <environment_variable name="SNPEFF_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
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14 </action>
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15 <action type="set_environment">
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16 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable>
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17 </action>
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18 </actions>
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19 </install>
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20 <readme>
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21 SnpEff and SnpSift
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22
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23 SnpEff ( http://snpeff.sourceforge.net/ ) is a variant annotation and effect prediction tool by Pablo Cingolani.
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24 It annotates and predicts the effects of variants on genes (such as amino acid changes).
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25
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26 This repository contains a tool_dependencies.xml file that downloads and installs SnpEff and SnpSift (SnpEff.jar and SnpSift.jar)
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27
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28 The install creates an environment variable: SNPEFF_JAR_PATH that contains the path to the jar files. Tools using this can generate a command line:
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29 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff -c \$SNPEFF_JAR_PATH/snpEff.config ...
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30
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31 The snpEff.config file is also installed, which specifies the default location for installed SnpEff genome databases:
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32 data_dir = ~/snpEff/data/
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33
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34 The location of a genome database can be set via the commandline option -dataDir. Tools using this can generate a command line:
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35 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir path_to_data_directory snpeff_database_name input.vcf
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36
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37 Another way to change the location of data_dir would be to create a symbolic link in the galaxy HOME directory:
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38 ln -s genome_data_path/snpEff ~/snpEff
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39
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40 SnpEff citation:
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41 "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly 6(2):80-92, 2012
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42
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43 SnpSift citation:
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44 "Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3:35, 2012.
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45 </readme>
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46 </package>
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47 </tool_dependency>
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