StarAMR-related DBs in Galaxy

[bebatut]

Hi,

I have a question regarding managing StarAMR-related DBs in Galaxy.
I do not see any data tables in the staramr folder and any DM.
How do you manage the DBs then?

We would like to update the DBs on usegalaxy.fr.

Thanks for your help.

Bérénice

[apetkau]

Hello Bérénice,

Yes, there are no data tables in Galaxy. Staramr by default uses database files that are distributed with the Python package (e.g., in the staramr-0.10.0/staramr/databases/data/dist directory in https://files.pythonhosted.org/packages/ea/54/a7c31d04eee72a914fa5be58fc057230a1bdb27e4fa3ebfbe475fb251551/staramr-0.10.0.tar.gz)

The staramr command-line tool includes the ability to download different versions of the underlying resfinder/pointfinder/plasmidfinder database files into a directory (staramr db build --dir db), and then use this directory for staramr (staramr search -d db).

However, we have not had the time to implement a tool in Galaxy to manage different versions of the staramr databases, which means updating is a bit more difficult.

It is still possible by activating the conda environment and running staramr db update --update-default to update the database files in the installed staramr code in conda. But that might not be the direction you wish to take.

Also, there is no guarantee that the updated database files will work with staramr since there might be incompatible changes. The way I have been handling database updates is to first test to make sure staramr is still working properly with any updated databases, and then make a new release of staramr.