Galaxy installation

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

• 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

• 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.galaxy_0.9.4/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.

• 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)

• 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:

galaxy.reload()