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annotate tool_dependencies.xml @ 14:ef4598ea7179

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Add SnpSift dependency
author Jim Johnson <jj@umn.edu>
date Fri, 21 Sep 2012 16:00:25 -0500
parents d57983929080
children bd23bbee9883
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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="3.0">
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4 <install version="1.0">
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5 <actions>
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6 <action type="shell_command">wget http://sourceforge.net/projects/snpeff/files/snpEff_v3_0_core.zip; unzip snpEff_v3_0_core.zip; mv snpEff_3_0 snpEff</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>$INSTALL_DIR</destination_directory>
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10 </action>
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12 <action type="set_environment">
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13 <environment_variable name="JAVA_JAR_PATH" action="prepend_to">$INSTALL_DIR/snpEff</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">$INSTALL_DIR/snpEff/scripts</environment_variable>
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17 </action>
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18 </actions>
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19 </install>
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20 <readme>
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21 </readme>
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22 </package>
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23 <package name="SnpSift" version="1.7">
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24 <install version="1.0">
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25 <actions>
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26 <action type="shell_command">mkdir -p SnpSift; cd SnpSift; wget http://sourceforge.net/projects/snpeff/files/SnpSift_v1_7.jar</action>
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27 <action type="set_environment">
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28 <environment_variable name="JAVA_JAR_PATH" action="prepend_to">$INSTALL_DIR/SnpSift</environment_variable>
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29 </action>
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30 </actions>
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31 </install>
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33 </tool_dependency>
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