Skip to content

feat(gtdbtk): add new r232 gtdbtk database #2039

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
prototaxites merged 5 commits into from
May 7, 2026
Merged

feat(gtdbtk): add new r232 gtdbtk database #2039

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
5b285a6
feat(gtdbtk): add gtdbtk database
prototaxites May 7, 2026
b2aa521
fix: update README
prototaxites May 7, 2026
d51b5c0
Merge branch 'mag' into mag_gtdbtk_new
prototaxites May 7, 2026
d5fccef
Update README.md
prototaxites May 7, 2026
2de562b
fix: re-name file correctly
prototaxites May 7, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 5 additions & 2 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -74,10 +74,13 @@ Which resulted in a last line of the log as

And then the `test/` directory was tarred to create `minigut_cat.tar.gz`.

We have uploaded a copy of the official [GTDB-Tk mock database](https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/gtdbtk_package/mockup_db/) to this repository for use while testing mag and the nf-core GTDB modules - this significantly improves the run-time of tests as the GTDB server can be very slow.
### GTDB-Tk

We have uploaded a copy of the official [GTDB-Tk mock database](https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/gtdbtk_package/mockup_db/) to this repository for use while testing mag and the nf-core GTDB modules - this significantly improves the run-time of tests as the GTDB server can be very slow.

The database is available as a gzipped tarball at:
- `databases/gtdbtk/gtdbtk_mockup_20250422.tar.gz`
- (r232, latest) `databases/gtdbtk/gtdbtk_mockup_r232_20260507.tar.gz`
- (r226) `databases/gtdbtk/gtdbtk_mockup_20250422.tar.gz`

### GUNC

Expand Down
Binary file added databases/gtdbtk/gtdbtk_mockup_r232_20260507.tar.gz
View file
Open in desktop
Copy link
Copy Markdown
Contributor

@mashehu mashehu May 7, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

i am guessing there is no chance in making this even smaller?

Copy link
Copy Markdown
Author

@prototaxites prototaxites May 7, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This is the small version of the 56Gb database the tool requires, as provided by the developers. I think it's about as minimal as can be...

Binary file not shown.