comparison tool_dependencies.xml @ 0:cbb49b5bc43f draft

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0:cbb49b5bc43f

<?xml version="1.0"?>
<tool_dependency>
    <package name="bwa" version="0.7.12">
        <repository changeset_revision="67aa12c8d449" name="package_bwa_0_7_12" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="samtools" version="1.2">
        <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="python" version="2.7.10">
        <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="bwameth" version="0.20">
        <install version="1.0">
            <actions>
                <action type="setup_python_environment">
                    <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="python" version="2.7.10" />
                    </repository>
                </action>
                <action type="shell_command">git clone https://github.com/brentp/bwa-meth</action>
                <action type="shell_command">git reset --hard 7dfec747105b9fa2cf1678bf5f67e860a0155d0e</action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
                </action>
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action>
             </actions>
         </install>
         <readme>
            Installation of bwa-meth from Brent Pedersen
            https://github.com/brentp/bwa-meth
         </readme>
     </package>
</tool_dependency>