Gtdbtk update and make it actually work#7987
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paulzierep
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May 19, 2026
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- Remove picrust2 commit from branch
- Make
place_speciesnon optional (if tests work with the option its ok, but I could not make that work, seems like current DB logic needs it). - Update to new DB and mockDB see #7983
| --prefix gtdbtk | ||
| --cpus "\${GALAXY_SLOTS:-4}" | ||
| --tmpdir tmp_dir | ||
| $advanced.place_species |
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in my test run, tool does not work without that param, similar to --skip_ani_screen
| ]]></command> | ||
| <inputs> | ||
| <param name="input" type="data" format="fasta,fasta.gz" multiple="true" label="Fasta (Genome) files"/> | ||
| <param name="gtdbtk_db" type="select" label="GTDB-Tk database" help="This version of GTDB-Tk requires GTDB version 226. Please contact your service administrator if this version is not available to select."> |
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We got the following error report:
This PR updates the tool and removes the --skip_ani_screen
I used the following prompt to update the tool:
Details
Please make a plan to update the Galaxy tool(s) in the tools/gtdbtk directory.We also got this error that needs to be validated and fixed:
adjustments
The --prefix is useless in the Galaxy context, as filenames do not get exposed to the user. This option could be used in the command section