view tool_dependencies.xml @ 20:ad06a6752350 draft

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<tool_dependency>
    <package name="virana_python" version="1.0">
        <install version="1.0">
            <actions>
                <action type="download_by_url">git clone -b master https://github.com/schelhorn/virana.git</action>
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
                <action type="set_environment">
                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
    </package>
    <package name="samtools" version="0.1.19">
        <install>
            <actions>
                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
                <action type="shell_command">make</action>
                <action type="move_file">
                    <source>samtools</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
    </package>
    <package name="bwa" version="0.7.4">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://sourceforge.net/projects/bio-bwa/files/bwa-0.7.4.tar.bz2 </action>
                <action type="shell_command">make</action>
                <action type="move_file">
                    <source>bwa</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
    </package>
    
    <package name="STAR" version="2.3.0" >
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://rna-star.googlecode.com/files/STAR_2.3.0e.tgz</action>
                <action type="move_file">
                    <source>STAR</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
    
    </package>
    <package name="lastz" version="1.02.00" >
        <install version="1.0">
            <actions>
                <action type="download_by_url" target_filename="lastz-distrib-1.02.00.tar.gz">http://www.bx.psu.edu/miller_lab/dist/lastz-1.02.00.tar.gz</action>
                <action type="shell_command">make</action>
                <action type="move_file">
                         <source>src/lastz</source>
                         <destination>$INSTALL_DIR/bin</destination>
                     </action>
                     <action type="move_file">
                         <source>src/lastz_D</source>
                         <destination>$INSTALL_DIR/bin</destination>
                     </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
    </package>
    <package name="jalview" version="2.8" >
        <install version="1.0">
            <actions>
                <action type="shell_command">git clone -b jalview https://github.com/schelhorn/virana.git</action>
                <action type="shell_command">mkdir $GALAXYROOT/tool-data/shared/jalview</action>
                <action type="shell_command">mkdir $GALAXYROOT/tool-data/shared/jalview/lib</action>
                <action type="move_file">
                         <source>jalview/jalview.jar</source>
                         <destination>$GALAXYROOT/tool-data/shared/jalview</destination>
                     </action>
                     <action type="move_directory_files">
                         <source_directory>jalview/lib</source_directory>
                         <destination_directory>$GALAXYROOT/tool-data/shared/jalview/lib</destination_directory>
                     </action>
            </actions>
        </install>
    </package>

</tool_dependency>