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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="clinod" version="1.3">
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4 <install version="1.0">
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5 <actions_group>
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6 <!-- Download the JAR, and SNNS binary for 64bit Linux -->
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7 <actions os="linux" architecture="x86_64">
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8 <!-- Main JAR file -->
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9 <!-- Original URL http://www.compbio.dundee.ac.uk/www-nod/downloads/clinod-1.3.jar -->
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10 <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>
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11 <action type="move_file"><source>clinod-1.3.jar</source><destination>$INSTALL_DIR/</destination></action>
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12 <!-- clinod requires the SNNS Batch Interpreter v1.0 executable -->
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13 <!-- Original URL http://www.ra.cs.uni-tuebingen.de/downloads/SNNS/SNNSv4.3.tar.gz -->
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14 <action type="download_file" sha256sum="54bf92d23e9198f9030a3c3d2b741472e9b8660b27d3b419ade6393b1ebf6f62" target_filename="SNNSv4.3.tar.gz">https://depot.galaxyproject.org/software/SNNS/SNNS_4.3_linux_x64.tar.gz</action>
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15 <action type="shell_command">tar -zxvf SNNSv4.3.tar.gz SNNSv4.3/tools/bin/x86_64-pc-unknown-linux-gnuoldld/batchman</action>
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16 <action type="move_file"><source>SNNSv4.3/tools/bin/x86_64-pc-unknown-linux-gnuoldld/batchman</source><destination>$INSTALL_DIR/</destination></action>
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17 <!-- Use the BioConda Python wrapper script to put 'clinod' in the install dir -->
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18 <action type="download_file" sha256sum="54de81f6ce9a30cee29a63b400d9a365c4a27d6efffa0096f3adcd91c1ce9066" target_filename="clinod">https://raw.githubusercontent.com/bioconda/bioconda-recipes/487d5fd2d993de578c9380d8da7a0dd0405836e7/recipes/clinod/clinod.py</action>
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19 <action type="shell_command">chmod a+x ./clinod</action>
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20 <action type="move_file"><source>clinod</source><destination>$INSTALL_DIR/</destination></action>
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21 </actions>
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22 <actions>
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23 <action type="shell_command">echo "ERROR: Automated installation on your operating system and CPU architecture combination is not yet supported."</action>
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24 <action type="shell_command">echo "Your machine details (the output from 'uname' and 'arch'):"</action>
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25 <action type="shell_command">uname</action>
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26 <action type="shell_command">arch</action>
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27 <action type="shell_command">echo "Please report this via https://github.com/peterjc/pico_galaxy/issues - thank you!"</action>
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28 <action type="shell_command">false</action>
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29 <!-- The 'false' command will return an error, so Galaxy should treat this as a failed install -->
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30 </actions>
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31 <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. -->
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32 <!-- Set environment variable $CLINOD so wrapper knows where to look -->
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33 <action type="set_environment">
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34 <environment_variable name="CLINOD" action="set_to">$INSTALL_DIR/</environment_variable>
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35 </action>
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36 </actions_group>
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37 </install>
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38 <readme>
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39 Downloads and installs the command line NoD (clinod) JAR file and the binary
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40 dependency batchman, and sets $CLINOD to the folder used.
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41
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42 We could download, compile and install the SNNS Batch Interpreter v1.0 executable
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43 (batchman) from Stuttgart Neural Network Simulator (SNNS) v4.2. However, we simplify
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44 this by downloading SNNS v4.3 which includes the precompiled copy of batchman.
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45
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46 For more details, see:
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47 http://www.compbio.dundee.ac.uk/www-nod/downloads.jsp
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48
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49 Additionally, to match the BioConda package a wrapper script clinod is also
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50 installed, see https://anaconda.org/bioconda/clinod and recipe source at
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51 https://github.com/bioconda/bioconda-recipes/tree/master/recipes/clinod
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52 </readme>
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53 </package>
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54 </tool_dependency>
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