comparison tools/clinod/tool_dependencies.xml @ 7:f61366a4a14e draft

v0.0.10 Internal changes to command line handling

6:77cfe958b5ea

<?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.

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

7:f61366a4a14e

<?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>$INSTALL_DIR/</destination></action>
                    <!-- clinod requires the SNNS Batch Interpreter v1.0 executable -->
                    <!-- Original URL http://www.ra.cs.uni-tuebingen.de/downloads/SNNS/SNNSv4.3.tar.gz -->
                    <action type="download_file" sha256sum="54bf92d23e9198f9030a3c3d2b741472e9b8660b27d3b419ade6393b1ebf6f62" target_filename="SNNSv4.3.tar.gz">https://depot.galaxyproject.org/software/SNNS/SNNS_4.3_linux_x64.tar.gz</action>
                    <action type="shell_command">tar -zxvf SNNSv4.3.tar.gz</action>
                    <action type="move_file"><source>SNNSv4.3/tools/bin/x86_64-pc-unknown-linux-gnuoldld/batchman</source><destination>$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.

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