“Quick” Guide for Experts

  1. If you have questions about why a certain procedure is being recommended, then please refer to the introduction or other relevant chapter of the manual for more details.
  2. Configure a new MIT StarCluster template.
    • You only need a single node.
    • Create a new EBS volume and assign it to your cluster template.
  3. Log into an EC2 instance created with your StarCluster template.
  4. Create a Python virtual environment somewhere (maybe at the mount point for the EBS volume which you created).
  5. Create a galaxy-python directory at your EBS volume mount point or in a directory beneath it.
  6. Symlink the python executable in your virtual environment into the galaxy-python directory.
  7. Clone http://bitbucket.org/galaxy/galaxy-dist into a sibling directory of your galaxy-python directory.
  8. Follow the instructions at Configuring the Main Galaxy Server.
  9. Follow the instructions at Testing the Main Galaxy Server.
  10. Make a mental note of the Galaxy serer’s unruliness mentioned in Stopping the Main Galaxy Server.
  11. Follow the instructions at Configuring the Galaxy Tool Shed Server.
  12. Follow the instructions at Testing the Galaxy Tool Shed Server.
  13. Follow the instructions at Securing the Galaxy Servers.
  14. Follow the instructions at Connecting the Galaxy Tool Shed to the Main Server.
  15. Follow the instructions at Testing the Tool Shed Connection.
  16. Acquire the sources for the tool you are trying to install. (Maybe dump them into a sibling directory of galaxy-dist.)
  17. Configure and build any binaries which you need.
  18. If the sources are Pythonically-packaged, then consider building a setuptools-style egg package, as Galaxy can be configured to use eggs on launch. If you need help, then please take at Building Eggs.
  19. Use the instructions at Creating Tool Categories and Adding a New Tool Repository, if you are not already familiar with the operation of a Galaxy tool shed.
  20. To learn how to find and edit an uploaded repo on the server, please see Editing a Tool Repository.
  21. Use the instructions at Refreshing Tool Shed Records, if you need to know how to update the Galaxy toolshed’s view of your changes.
  22. Use the instructions at Deployment of New Tools, if you need to know how to transport your tool from the toolshed server to the main server.

Previous topic

Welcome to Galaxy-on-StarCluster’s documentation!

Next topic

Introductory Discussion

This Page