view tool_dependencies.xml @ 44:b71da02aa36a draft

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<?xml version="1.0"?>
<tool_dependency>
    <package name="numpy" version="1.7">
        <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="pysam" version="0.7.6">
        <repository changeset_revision="247e5e5bee87" name="package_pysam_0_7_6" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="freetype" version="2.4">
        <repository changeset_revision="fe5cfaf931ff" name="package_freetype_2_4" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
    </package>
    <package name="matplotlib" version="1.2">
        <repository changeset_revision="966f29c955b9" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
    </package>
    <package name="htseq" version="0.5.4p3">
        <install version="1.0">
            <actions>
                <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
                <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
                <action type="set_environment_for_install">
                        <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
                            <package name="numpy" version="1.7" />
                        </repository>
                        <repository changeset_revision="247e5e5bee87" name="package_pysam_0_7_6" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
                            <package name="pysam" version="0.7.6" />
                        </repository>
                        <repository changeset_revision="fe5cfaf931ff" name="package_freetype_2_4" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                            <package name="freetype" version="2.4" />
                        </repository>
                        <repository changeset_revision="966f29c955b9" name="package_matplotlib_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                            <package name="matplotlib" version="1.2" />
                        </repository>
                </action>
                <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p3.tar.gz</action>
                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
                <action type="set_environment">
                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), pysam and the Numpy Python package. 
            Note this uses the matplotlib lite version dependent on the lite version of numpy - no atlas compilation 
        </readme>
    </package>
</tool_dependency>