comparison tool_dependencies.xml @ 0:378fc267bd0e draft default tip

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0:378fc267bd0e

<?xml version="1.0"?>
<tool_dependency>
    <package name="velvet" version="1.2.10">
        <install version="1.0">
            <actions>
                <action type="shell_command">git clone git://github.com/dzerbino/velvet.git velvet</action>
                <action type="shell_command">git reset --hard 5cea317b4ec5c3f0fd2931321bc7231d8a250682</action>
                <action type="shell_command">make -i CATEGORIES=4 MAXKMERLENGTH=191 OPENMP=1</action>
                <action type="shell_command">mkdir scripts</action>
                <action type="shell_command">find contrib/[a-z]* -type f -name '*.p?' -exec cp -p {} scripts ";"</action>
                <action type="shell_command">cp -rp contrib/VelvetOptimiser*/VelvetOpt* scripts</action>
                <action type="shell_command">ls scripts</action>
                <action type="move_file">
                    <source>velvetg</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>velveth</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_directory_files">
                    <source_directory>scripts</source_directory>
                    <destination_directory>$INSTALL_DIR/scripts</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable>
                </action>
                <action type="set_environment">
                    <environment_variable name="MAXKMERLENGTH" action="set_to">191</environment_variable>
                </action>
                <action type="set_environment">
                    <environment_variable name="CATEGORIES" action="set_to">4</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            Velvet is a sequence assembler for very short reads.
            http://www.ebi.ac.uk/~zerbino/velvet/
            This installs the velvet assembler version 1.2.10 and contributed scripts including VelvetOptimiser.pl 
        </readme>
    </package>
</tool_dependency>