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author qfab
date Thu, 29 May 2014 20:35:40 -0400
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<?xml version="1.0"?>
<tool_dependency>
        <package name="numpy" version="1.8.1">
            <repository changeset_revision="36659940cecb" name="package_numpy_1_8" owner="qfab" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" />
        </package>
        <package name="pycogent" version="1.5.2">
            <install version="1.0">
                <actions>
                    <action type="download_by_url">http://sourceforge.net/projects/pycogent/files/PyCogent/1.5.2/PyCogent-1.5.2.tgz/download</action>
                    <action type="make_directory">$INSTALL_DIR/cogent</action>
                    <action type="set_environment_for_install">
                       <repository changeset_revision="36659940cecb" name="package_numpy_1_8" owner="qfab" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" >
                          <package name="numpy" version="1.8.1" />
                        </repository>
                    <action type="shell_command">
                      python -c "import numpy; print numpy.version.version" &amp;&amp; env >> /opt/galaxy/log.txt:
                    </action>
                    </action>
                    <action type="shell_command">
                        python setup.py build_ext -if
                    </action>
                    <action type="move_directory_files">
                        <source_directory>cogent</source_directory>
                        <destination_directory>$INSTALL_DIR/cogent/</destination_directory>
                    </action> 
                    <action type="set_environment">
                       <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
                       <environment_variable action="set_to" name="PATH_PYCOGENT">$INSTALL_DIR</environment_variable>
                       <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
                       <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable> 
                    </action>
                </actions>
            </install>
            <readme>It is required to install a numpy python package (here numpy python package version 1.8.1) before installing the pycogent package.</readme>
        </package>
</tool_dependency>