view tool_dependencies.xml @ 34:b51c36920d7b draft

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<?xml version="1.0"?>
<tool_dependency>
    
    <!-- PACKAGES -->
    <package name="R" version="3.1.0">
        <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    
    <package name="samtools" version="0.1.19">
        <repository changeset_revision="233326db3402" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>

    
    <package name="bcftools" version="2">
        <repository changeset_revision="5f9ba601748e" name="bcftools" owner="iuc" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
        <readme>Let's see where this msg appears...bcftools</readme>
    </package>
    
    <!--
    <package name="snpeff" version="3.4">
        <repository name="package_snpeff_3_4" owner="jjohnson" prior_installation_required="TRUE" />
        <readme>Let's see where this msg appears...snpeff</readme>
    </package>
    
    <package name="varscan" version="2">
        <repository name="varscan_version_2" owner="devteam" prior_installation_required="TRUE" />
        <readme>Let's see where this msg appears...varscan</readme>
    </package>
    -->
    
    <!-- ENV -->
    
    <set_environment>
        <environment_variable action="set_to" name="TOOL_DIR">$REPOSITORY_INSTALL_DIR</environment_variable>
    </set_environment>
    <!--
    <set_environment>
        <environment_variable action="set_to" name="JAR_PATH1">$JAVA_JAR_PATH</environment_variable>
    </set_environment>
    <set_environment>
        <environment_variable action="set_to" name="JAR_PATH2">$SNPEFF_JAR_PATH</environment_variable>
    </set_environment>
    -->

    <!--<environment_variable action="set_to" name="VARSCAN_DIR">$JAVA_JAR_PATH</environment_variable>-->
    
</tool_dependency>