Mercurial > repos > peterjc > clinod
comparison tools/clinod/tool_dependencies.xml @ 7:f61366a4a14e draft
v0.0.10 Internal changes to command line handling
author | peterjc |
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date | Tue, 16 May 2017 08:50:43 -0400 |
parents | 9485cdfca57e |
children | 4863b1dbe8f0 |
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6:77cfe958b5ea | 7:f61366a4a14e |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <tool_dependency> | 2 <tool_dependency> |
3 <package name="clinod" version="1.3"> | 3 <package name="clinod" version="1.3"> |
4 <install version="1.0"> | 4 <install version="1.0"> |
5 <actions> | 5 <actions_group> |
6 <!-- Download the JAR, and SNNS binary for 64bit Linux --> | |
7 <actions os="linux" architecture="x86_64"> | |
8 <!-- Main JAR file --> | |
9 <!-- Original URL http://www.compbio.dundee.ac.uk/www-nod/downloads/clinod-1.3.jar --> | |
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> | |
11 <action type="move_file"><source>clinod-1.3.jar</source><destination>$INSTALL_DIR/</destination></action> | |
12 <!-- clinod requires the SNNS Batch Interpreter v1.0 executable --> | |
13 <!-- Original URL http://www.ra.cs.uni-tuebingen.de/downloads/SNNS/SNNSv4.3.tar.gz --> | |
14 <action type="download_file" sha256sum="54bf92d23e9198f9030a3c3d2b741472e9b8660b27d3b419ade6393b1ebf6f62" target_filename="SNNSv4.3.tar.gz">https://depot.galaxyproject.org/software/SNNS/SNNS_4.3_linux_x64.tar.gz</action> | |
15 <action type="shell_command">tar -zxvf SNNSv4.3.tar.gz</action> | |
16 <action type="move_file"><source>SNNSv4.3/tools/bin/x86_64-pc-unknown-linux-gnuoldld/batchman</source><destination>$INSTALL_DIR/</destination></action> | |
17 </actions> | |
18 <actions> | |
19 <action type="shell_command">echo "ERROR: Automated installation on your operating system and CPU architecture combination is not yet supported."</action> | |
20 <action type="shell_command">echo "Your machine details (the output from 'uname' and 'arch'):"</action> | |
21 <action type="shell_command">uname</action> | |
22 <action type="shell_command">arch</action> | |
23 <action type="shell_command">echo "Please report this via https://github.com/peterjc/pico_galaxy/issues - thank you!"</action> | |
24 <action type="shell_command">false</action> | |
25 <!-- The 'false' command will return an error, so Galaxy should treat this as a failed install --> | |
26 </actions> | |
27 <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. --> | |
6 <!-- Set environment variable $CLINOD so wrapper knows where to look --> | 28 <!-- Set environment variable $CLINOD so wrapper knows where to look --> |
7 <action type="set_environment"> | 29 <action type="set_environment"> |
8 <environment_variable name="CLINOD" action="set_to">$INSTALL_DIR</environment_variable> | 30 <environment_variable name="CLINOD" action="set_to">$INSTALL_DIR/</environment_variable> |
9 </action> | 31 </action> |
10 <!-- clinod requires the SNNS Batch Interpreter v1.0 executable --> | 32 </actions_group> |
11 <action type="shell_command">wget http://www.ra.cs.uni-tuebingen.de/downloads/SNNS/SNNSv4.3.tar.gz</action> | |
12 <action type="shell_command">tar -zxvf SNNSv4.3.tar.gz</action> | |
13 <action type="move_file"><source>SNNSv4.3/tools/bin/x86_64-pc-unknown-linux-gnuoldld/batchman</source><destination>$INSTALL_DIR/</destination></action> | |
14 <!-- clinod itself is just a JAR file --> | |
15 <action type="shell_command">wget http://www.compbio.dundee.ac.uk/nod/downloads/clinod-1.3.jar</action> | |
16 <!-- Don't need to move it, $INSTALL_DIR is the current directory | |
17 <action type="move_file"><source>clinod-1.3.jar</source><destination>$INSTALL_DIR</destination></action> | |
18 --> | |
19 </actions> | |
20 </install> | 33 </install> |
21 <readme> | 34 <readme> |
22 Downloads and installs the command line NoD (clinod) JAR file and the binary | 35 Downloads and installs the command line NoD (clinod) JAR file and the binary |
23 dependency batchman, and sets $CLINOD to the folder used. | 36 dependency batchman, and sets $CLINOD to the folder used. |
24 | 37 |
29 For more details, see: | 42 For more details, see: |
30 http://www.compbio.dundee.ac.uk/www-nod/downloads.jsp | 43 http://www.compbio.dundee.ac.uk/www-nod/downloads.jsp |
31 </readme> | 44 </readme> |
32 </package> | 45 </package> |
33 </tool_dependency> | 46 </tool_dependency> |
34 |