Mercurial > repos > lparsons > htseq_count

view tool_dependencies.xml @ 16:227f9d3f0e32 draft

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Updated HTSeq package to version 0.6.1, fixed input format string, updated dependency definitions
author lparsons
date Fri, 11 Apr 2014 15:05:28 -0400
parents 265ca0f35789
children d5edaf8dc974
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<?xml version="1.0"?>
<tool_dependency>

    <package name="numpy" version="1.7.1">
        <repository changeset_revision="0c288abd2a1e" name="package_numpy_1_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>

    <package name="samtools" version="0.1.19">
        <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>

    <package name="htseq" version="0.6.1">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.6.1.tar.gz</action>
                <!-- populate the environment variables from the dependend repos -->
                <action type="set_environment_for_install">
                    <repository changeset_revision="0c288abd2a1e" name="package_numpy_1_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu">
                        <package name="numpy" version="1.7.1" />
                   </repository>
                </action>
                <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="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), and the Nympy Python package.
        </readme>
    </package>

</tool_dependency>