view tools/clinod/tool_dependencies.xml @ 8:4863b1dbe8f0 draft

"Update all the pico_galaxy tools on main Tool Shed"

<?xml version="1.0"?>
<tool_dependency>
    <package name="clinod" version="1.3">
        <install version="1.0">
            <actions_group>
                <!-- Download the JAR, and SNNS binary for 64bit Linux -->
                <actions os="linux" architecture="x86_64">
                    <!-- Main JAR file -->
                    <!-- Original URL http://www.compbio.dundee.ac.uk/www-nod/downloads/clinod-1.3.jar -->
                    <action type="download_file" sha256sum="45d80662ba109a7af28aeafcfb2ca417a7d575ac3700f69bd40965a69d41e072" target_filename="clinod-1.3.jar">https://depot.galaxyproject.org/software/clinod/clinod_1.3_src_all.jar</action>
                    <action type="move_file"><source>clinod-1.3.jar</source><destination>$INSTALL_DIR/</destination></action>
                    <!-- clinod requires the SNNS Batch Interpreter v1.0 executable -->
                    <!-- Original URL http://www.ra.cs.uni-tuebingen.de/downloads/SNNS/SNNSv4.3.tar.gz -->
                    <action type="download_file" sha256sum="54bf92d23e9198f9030a3c3d2b741472e9b8660b27d3b419ade6393b1ebf6f62" target_filename="SNNSv4.3.tar.gz">https://depot.galaxyproject.org/software/SNNS/SNNS_4.3_linux_x64.tar.gz</action>
                    <action type="shell_command">tar -zxvf SNNSv4.3.tar.gz SNNSv4.3/tools/bin/x86_64-pc-unknown-linux-gnuoldld/batchman</action>
                    <action type="move_file"><source>SNNSv4.3/tools/bin/x86_64-pc-unknown-linux-gnuoldld/batchman</source><destination>$INSTALL_DIR/</destination></action>
                    <!-- Use the BioConda Python wrapper script to put 'clinod' in the install dir -->
                    <action type="download_file" sha256sum="54de81f6ce9a30cee29a63b400d9a365c4a27d6efffa0096f3adcd91c1ce9066" target_filename="clinod">https://raw.githubusercontent.com/bioconda/bioconda-recipes/487d5fd2d993de578c9380d8da7a0dd0405836e7/recipes/clinod/clinod.py</action>
                    <action type="shell_command">chmod a+x ./clinod</action>
                    <action type="move_file"><source>clinod</source><destination>$INSTALL_DIR/</destination></action>
                </actions>
                <actions>
                    <action type="shell_command">echo "ERROR: Automated installation on your operating system and CPU architecture combination is not yet supported."</action>
                    <action type="shell_command">echo "Your machine details (the output from 'uname' and 'arch'):"</action>
                    <action type="shell_command">uname</action>
                    <action type="shell_command">arch</action>
                    <action type="shell_command">echo "Please report this via https://github.com/peterjc/pico_galaxy/issues - thank you!"</action>
                    <action type="shell_command">false</action>
                    <!-- The 'false' command will return an error, so Galaxy should treat this as a failed install -->
                </actions>
                <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. -->
                <!-- 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>
            </actions_group>
        </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 batchman.

For more details, see:
http://www.compbio.dundee.ac.uk/www-nod/downloads.jsp

Additionally, to match the BioConda package a wrapper script clinod is also
installed, see https://anaconda.org/bioconda/clinod and recipe source at
https://github.com/bioconda/bioconda-recipes/tree/master/recipes/clinod
        </readme>
    </package>
</tool_dependency>