annotate tool_dependencies.xml @ 0:bd66bc0860db draft default tip

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2-dirty

<?xml version="1.0"?>
<tool_dependency>
    <package name="python" version="2.7">
        <repository changeset_revision="eb37ce21eef1" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    
    <package name="htseq" version="0.6.1">
        <repository changeset_revision="fbb72996807d" name="package_htseq_0_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    
    <package name="fuma" version="2.10.1">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://github.com/yhoogstrate/fuma/archive/6b79b9a958212b900dedda0247f84f696f81ec89.tar.gz</action>
                
                <action type="set_environment_for_install">
                     <repository changeset_revision="eb37ce21eef1" name="package_python_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="python" version="2.7" />
                    </repository>
                    
                   <repository changeset_revision="fbb72996807d" name="package_htseq_0_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="htseq" version="0.6.1" />
                    </repository>
                </action>
                
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action type="make_directory">$INSTALL_DIR/lib64/python</action>
                
                <action type="shell_command">
                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &amp;&amp;
                    python setup.py build                                                           &amp;&amp;
                    python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin
                    
                    ## Tests fails because the import of unittest goes wrong:
                    ## http://stackoverflow.com/questions/26893504/attributeerror-module-object-has-no-attribute-testcase
                    ## python setup.py test
                </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>
                    
                    <environment_variable action="set_to" name="FUMA_PATH">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="set_to" name="FUMA_ROOT_PATH">$INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            Downloads and installs FuMa.
            
            Prerequisites:
                - git
        </readme>
    </package>
</tool_dependency>