transferring tools/reference genomes from one galaxy instance to another

Hi. I was wondering if there is a streamline way to transfer the tools installed on one galaxy instance to another instance. I have been working on a galaxy instance for testing and we are now ready to migrate to our production galaxy both of which we are running on an HPC. Is there a streamline way to transfer the tools on the dev server to our prod server without having to re-install all the tools individually? Thanks.


We have made a tool for this called Ephemeris. You can use it to download a list of all tools from an instance and then automatically install all of them in the new one, training is here:

Reference genomes are slightly different, but I believe you can move them by copying all the required configuration and data files. Let us know if you need help with that.

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Follow up question:

When using Ephemeris to install the list of tools to our new galaxy instance do we need to manually create the tool panels that do not exist in the new galaxy instance or should the shed-install command be able to create the new panel id’s when it encounters a new one as it is reading the tool.yaml?

I assumed shed-install would be able to create all the necessary tool panels and place the proper tools in them because the tools.yaml has all that information but when running the command no new panel ids are being created in our new galaxy instance.

I assume you mean tool panel sections. Per the documentation ephemeris does not create them. I am not sure why is that, probably Galaxy lacks an API to do that programatically. (PRs welcome)

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