comparison rgweblogo/tool_dependencies.xml @ 17:baa6a37ed578 draft

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17:baa6a37ed578

<?xml version="1.0"?>
<tool_dependency>
    <package name="numpy" version="1.7.1">
        <repository changeset_revision="af9633757cf0" name="package_numpy_1_7" owner="blankenberg" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="ghostscript" version="9.07">
        <repository changeset_revision="10222a7db54c" name="package_ghostscript_9_07" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>

    <package name="package_weblogo" version="3.3">
        <install version="1.0">
            <actions>
                <!-- populate the environment variables from the dependend repos -->
                <action type="download_by_url">http://weblogo.googlecode.com/files/weblogo-3.3.tar.gz</action>
                <action type="shell_command">echo `ls -lt` &amp;&amp; echo `pwd`</action>
                
                <action type="set_environment_for_install">
                    <repository changeset_revision="c842299349c0" name="package_ghostscript_9_07" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                        <package name="ghostscript" version="9.07" />
                    </repository>
                    <repository changeset_revision="af9633757cf0" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                        <package name="numpy" version="1.7.1" />
                    </repository>
                </action>
                <!-- install weblogo -->
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action type="shell_command">export PYTHONPATH=$INSTALL_DIR/lib/python:$PYTHONPATH_NUMPY:$PYTHONPATH &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</environment_variable>
                    <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="set_to" name="WEBLOGO_PATH">$INSTALL_DIR/bin/weblogo</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            weblogo3 is a python version of the old weblogo2.8 or so. Requires numpy and ghostscript so these are installed if not already on your system - if that happens, please be patient
            while numpy compiles - especially if the ATLAS libraries are being installed - which is not at present.
        </readme>
     </package>
</tool_dependency>