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annotate tool_dependencies.xml @ 34:b51c36920d7b draft

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author stef
date Fri, 10 Oct 2014 10:13:55 -0400
parents 3419fc808193
children f1b32c09deaf
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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4 <!-- PACKAGES -->
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5 <package name="R" version="3.1.0">
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6 <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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7 </package>
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9 <package name="samtools" version="0.1.19">
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10 <repository changeset_revision="233326db3402" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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11 </package>
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14 <package name="bcftools" version="2">
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15 <repository changeset_revision="5f9ba601748e" name="bcftools" owner="iuc" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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16 <readme>Let's see where this msg appears...bcftools</readme>
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17 </package>
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19 <!--
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20 <package name="snpeff" version="3.4">
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21 <repository name="package_snpeff_3_4" owner="jjohnson" prior_installation_required="TRUE" />
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22 <readme>Let's see where this msg appears...snpeff</readme>
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23 </package>
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25 <package name="varscan" version="2">
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26 <repository name="varscan_version_2" owner="devteam" prior_installation_required="TRUE" />
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27 <readme>Let's see where this msg appears...varscan</readme>
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28 </package>
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31 <!-- ENV -->
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33 <set_environment>
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34 <environment_variable action="set_to" name="TOOL_DIR">$REPOSITORY_INSTALL_DIR</environment_variable>
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35 </set_environment>
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36 <!--
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37 <set_environment>
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38 <environment_variable action="set_to" name="JAR_PATH1">$JAVA_JAR_PATH</environment_variable>
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39 </set_environment>
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40 <set_environment>
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41 <environment_variable action="set_to" name="JAR_PATH2">$SNPEFF_JAR_PATH</environment_variable>
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42 </set_environment>
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43 -->
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45 <!--<environment_variable action="set_to" name="VARSCAN_DIR">$JAVA_JAR_PATH</environment_variable>-->
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47 </tool_dependency>