gtdbtk databases question [help wanted]

[cat-bro]

There is a new gtdbtk and no databases are available for it on Galaxy Australia yet because there is nothing in the gtdbtk_database_versioned - our previous entries have gone in the gtdbtk_database loc file.

This is the content of the gtdbtk_database data table:

value | name | path
-- | -- | --
release_207 | gtdbtk database release 207 | /mnt/custom-indices/gtdbtk_database/gtdb_tk_data_20220408
release202 | gtdbtk database release 202 | /mnt/custom-indices/gtdbtk_database/release202
release_207_v2 | gtdbtk database release 207_v2 | /mnt/custom-indices/gtdbtk_database/release_207_v2

The tool help text says This version of GTDB-Tk requires GTDB version 207 or 214

What I'm wondering is, can I make an entry in the gtdbtk_database_versioned that points to one of our 207 databases and if so, which one should I choose: 207 or 207_v2?

Ping @paulzierep

[paulzierep]

I updated the tool since it can only work with specific DBs - therefore it was not good that all tool versions saw all DB versions. Unfortunately, that required a change of the data table.
You should be able to add a manual entry to the gtdbtk_database_versioned table and point to release_207_v2. R207 is not compatible with tool 2.3.2 (according to https://ecogenomics.github.io/GTDBTk/installing/index.html).
There is also an updated DM for the tool that writes to the new table. But I understand that a duplicated large DB is not desired :)