View source for Galaxy installation

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

* [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:
  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_{{BioUML current version}}/glaunch.sh has +x attribute

* Restart BioUML server

* Galaxy analyses should appear in “Analyses” tab in the tree.

=== 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.

* If you want to create your own tools, refer to [[Creating Galaxy tool]] page.

[[Category:Installation]]
[[Category:Galaxy]]