Remove entries in Data Manager: all_fasta.

, ,
1

I am an admin on a local instance, trouble-shooting problems with using DataManager. Is it possible to remove entries in Data Manager, specifically all_fasta? I found an old post which says No. Is this still the case?

2

Welcome, @hughesd

Complicated question!!

Technically you can manually adjust anything that you want to This is how it was all done originally – additions, removals, corrections. You must be extremely careful but it is certainly possible.

You will need to have that all_fasta file itself but it could be empty (no local indexes) or have custom values that link into other custom lines in other custom tables.

But first, do you want to troubleshoot what is going wrong with the Data Manager itself? Was it sourced from the ToolShed? Are you doing other custom adjustments? Are you trying to remove/comment out bad entries that were added?

Or, you can just dive right it! Save a back up before you start!

We have some older administrative docs here with command instructions and general directly structure outlines.

Most of this is deprecated but the Data Resources section has mostly correct information as far as local tables are concerned. If you are also using the CVMFS mount, tread extra carefully. Save back copies to make reverting easier. I wrote and used those guides and might remember how they work if you have a question about the content.

XRef – these are the current definitive safe administrative guides.

Let’s start there! :slight_smile:

3

Many thanks @jennaj
Our Data Managers were sourced from the Tool Shed.
We used Create DBKey to add entries to __ dbkeys __ and all_fasta.
I hoped to find an option or Data Manager to delete a bad entry, but did not.
I found this earlier post, which I guess still applies:
https://biostar.usegalaxy.org/p/13591/index.html

1 Like
4

Hi @hughesd

Yes, that older post is still valid. An “undo” function is still pending. There are a few topics about that here, too, that I had forgot about yesterday, but this is probably the best one → Remove installed databases - #2 by jennaj. Notice how that was for a specific tool – and that it involved a few tables. Maybe good to know for later. In short, trace back through what the original DM touched and pick out your changes. Then restart the server.

For the DM you are using, there is less data to tidy up. It would be those two tables plus any associated genome indexes themselves such as the fasta + fasta.fai (although the data files would be ignored if the tables do not reference it, and you are not tool concerned about the storage space).

Glad you are working this out! Maybe someone will see this and take on a project for the undo tasks. The reason why this isn’t higher in priority is mostly that the administrators are using Ephemeris to load up genomes onto instances in a batch, or in response to tool installs. That is all done through PRs with built in checks on the public sites.

The undo would probably fit best into that application, for maybe the gxyadmin utility. If you know of anyone looking for a project, or anyone else reading this who is interested, this would be a good discrete project with a clear end goal and grateful users! Maybe for a grad student or someone looking to build up open source projects for their portfolio. They would get support from our team! I’m pitching now! :slight_smile: :hammer_and_wrench:

5

Thanks @jennaj for all the detail. I have much more confidence in this area now.

1 Like