annotate tools/clinod/tool_dependencies.xml @ 5:9485cdfca57e draft

v0.0.8 internal changes

<?xml version="1.0"?>
<tool_dependency>
    <package name="clinod" version="1.3">
        <install version="1.0">
            <actions>
                <!-- Set environment variable $CLINOD so wrapper knows where to look -->
                <action type="set_environment">
                    <environment_variable name="CLINOD" action="set_to">$INSTALL_DIR</environment_variable>
                </action>
                <!-- clinod requires the SNNS Batch Interpreter v1.0 executable -->
                <action type="shell_command">wget http://www.ra.cs.uni-tuebingen.de/downloads/SNNS/SNNSv4.3.tar.gz</action>
                <action type="shell_command">tar -zxvf SNNSv4.3.tar.gz</action>
                <action type="move_file"><source>SNNSv4.3/tools/bin/x86_64-pc-unknown-linux-gnuoldld/batchman</source><destination>$INSTALL_DIR/</destination></action>
                <!-- clinod itself is just a JAR file -->
                <action type="shell_command">wget http://www.compbio.dundee.ac.uk/nod/downloads/clinod-1.3.jar</action>
                <!-- Don't need to move it, $INSTALL_DIR is the current directory
                <action type="move_file"><source>clinod-1.3.jar</source><destination>$INSTALL_DIR</destination></action>
                -->
            </actions>
        </install>
        <readme>
Downloads and installs the command line NoD (clinod) JAR file and the binary
dependency batchman, and sets $CLINOD to the folder used.

We could download, compile and install the SNNS Batch Interpreter v1.0 executable
(batchman) from Stuttgart Neural Network Simulator (SNNS) v4.2. However, we simplify
this by downloading SNNS v4.3 which includes the precompiled copy of batch man.

For more details, see:
http://www.compbio.dundee.ac.uk/www-nod/downloads.jsp
        </readme>
    </package>
</tool_dependency>