Difference between revisions of "Galaxy installation"

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This page describes how to integrate Galaxy with installed BioUML server.
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This page describes how to integrate {{Galaxy}} with installed BioUML server.
  
* [http://galaxyproject.org/ Download Galaxy distribution] and unpack it somewhere. It usually contains galaxy_dist directory. Let’s say it’s $GALAXY_DIST
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* [http://wiki.galaxyproject.org/Admin/Get%20Galaxy/ Download Galaxy distribution] and unpack it somewhere. It usually contains galaxy_dist directory. Let’s say it’s $GALAXY_DIST
  
 
* Galaxy requires python eggs, starting galaxy server for the first time will acquire these dependencies. Run the following command from $GALAXY_DIST folder:
 
* Galaxy requires python eggs, starting galaxy server for the first time will acquire these dependencies. Run the following command from $GALAXY_DIST folder:
 
   sh run.sh
 
   sh run.sh
  
  After successful setup it will write "Starting server in PID", kill galaxy server with Ctrl^C.
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After successful setup it will write "Starting server in PID", kill galaxy server with Ctrl^C.
  
 
* Change ownership of $GALAXY_DIST folder:
 
* Change ownership of $GALAXY_DIST folder:
 
   chown -R tomcat6:tomcat6 $GALAXY_DIST
 
   chown -R tomcat6:tomcat6 $GALAXY_DIST
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* Create and change ownership of .python-eggs folder usually located in tomcat home:
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  mkdir /usr/share/tomcat6/.python-eggs
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  chown -R tomcat6:tomcat6 /usr/share/tomcat6/.python-eggs
  
 
* Visit $SERVER_PATH/analyses. There should be “Galaxy” folder with “default.config” file (create it if absent). The file content should be the following:
 
* Visit $SERVER_PATH/analyses. There should be “Galaxy” folder with “default.config” file (create it if absent). The file content should be the following:
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* Replace $GALAXY_DIST with your path and optionally change galaxy.tmp
 
* Replace $GALAXY_DIST with your path and optionally change galaxy.tmp
  
* Make sure that $SERVER_PATH/plugins/ru.biosoft.galaxy_0.9.4/glaunch.sh has +x attribute
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* Make sure that $SERVER_PATH/plugins/ru.biosoft.workbench_{{BioUML current version}}/glaunch.sh has +x attribute
  
 
* Restart BioUML server
 
* Restart BioUML server
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* Note that only some Galaxy tools work “out-of-the-box”. For many of them additional software or data files (like genome indexes, etc.) must be installed and properly configured.
 
* Note that only some Galaxy tools work “out-of-the-box”. For many of them additional software or data files (like genome indexes, etc.) must be installed and properly configured.
  
* List of available Galaxy tools is in $GALAXY_DIST/tool_conf.xml. Tool files are located inside $GALAXY_DIST/tools directory. So you may try to create your own tools there (or disable existing ones)
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* If you want to create your own tools, refer to [[Creating Galaxy tool]] page.
 
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* To reload Galaxy configuration (after you changed tool_conf.xml or xml-files of specific tools) you should log in to BioUML as administrator select “Script” tab (in right-bottom set of tabs) and type there the following command:
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galaxy.reload()
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[[Category:Installation]]
 
[[Category:Installation]]
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[[Category:Galaxy]]

Latest revision as of 11:31, 30 July 2013

This page describes how to integrate Galaxy with installed BioUML server.

  • Galaxy requires python eggs, starting galaxy server for the first time will acquire these dependencies. Run the following command from $GALAXY_DIST folder:
 sh run.sh

After successful setup it will write "Starting server in PID", kill galaxy server with Ctrl^C.

  • Change ownership of $GALAXY_DIST folder:
 chown -R tomcat6:tomcat6 $GALAXY_DIST
  • Create and change ownership of .python-eggs folder usually located in tomcat home:
 mkdir /usr/share/tomcat6/.python-eggs
 chown -R tomcat6:tomcat6 /usr/share/tomcat6/.python-eggs
  • Visit $SERVER_PATH/analyses. There should be “Galaxy” folder with “default.config” file (create it if absent). The file content should be the following:
name = Galaxy
class = ru.biosoft.galaxy.GalaxyDataCollection
plugins=ru.biosoft.galaxy
galaxy.path = $GALAXY_DIST
galaxy.tmp = /tmp
  • Replace $GALAXY_DIST with your path and optionally change galaxy.tmp
  • Make sure that $SERVER_PATH/plugins/ru.biosoft.workbench_2023.3/glaunch.sh has +x attribute
  • Restart BioUML server
  • Galaxy analyses should appear in “Analyses” tab in the tree.

[edit] Notes

  • Note that only some Galaxy tools work “out-of-the-box”. For many of them additional software or data files (like genome indexes, etc.) must be installed and properly configured.
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