From BioUML platform
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:
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_2020.4/glaunch.sh has +x attribute
- Restart BioUML server
- Galaxy analyses should appear in “Analyses” tab in the tree.
- 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.