Galaxy installation

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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_2018.2/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.
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