update BUSCO and fix --miniprot parameter

[rlibouba]

Hello, I've opened this PR to update the BUSCO version and fix an error on the --miniprot parameter (#6147).
Thank you! Have a good day!

[mvdbeek]

busco: error: unrecognized arguments: --update-data, I guess this was removed at some point between version 5.5.0 and 5.7.1 ?

[Hymenium]

Yes, it seems that this command was removed in v5.6.1, although I can't easily find any documentation regarding the change.

[Hymenium]

Note that the Augustus/MetaEuk parameter cannot select for MetaEuk currently. The options are coded to yes and no for using Augustus as an alternative, and no --metaeuk parameter is ever issued.
e.g.

tools-iuc/tools/busco/busco.xml

Line 53 in 6853ad9

#if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes':

[Hymenium]

This looks good.

It may help users to put some information somewhere about BUSCO using the Prodigal predictor for prokaryotic data.

[rlibouba]

Yes, I can add a helper to indicate this. I'm trying to fix the errors in the tests. I'll do a general commit with all the changes

[Hymenium]

Thank you. I saw that some tests had failed but I can't see any error messages to see what failed. Other than the change of default predictor and some formatting changes between version, it's hard to understand why the tests would fail.

[bgruening]

@rlibouba anything we can help here?

[rlibouba]

Hi @bgruening, I've noticed two different errors.
The first relates to the use of miniprot. The error I got was error: local variable 'target_id' referenced before assigment. A issues is open (https://gitlab.com/ezlab/busco/-/issues/744). Three of us have reported this error.

For the second, the error is multiple repeat at position 351 (line 7, column 3). Perhaps this is linked to the Galaxy code? Do you have any ideas?

[bgruening]

For the second, the error is multiple repeat at position 351 (line 7, column 3). Perhaps this is linked to the Galaxy code? Do you have any ideas?

This does not seem to be an error, but it fails because of:

2024-08-20 15:19:16 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead. 

[abretaud]

I think it's not related to this warning, if you look at the test 1 you only have the multiple repeat at position. Google says it's a regex related error, but I don't see where it could come from in the tool code 🤔

[Hymenium]

Could it be related to how the results files are compared in the tests? In the previous results files some special characters are escaped (e.g. \* vs *).

[bgruening]

Please take it out of draft if you are ready.

[Hymenium]

Is there any real test for the .gff output? The first line seems to be checked, but this is created in the tool script.

[bgruening]

@Hymenium we could add more asserts but files like tools/busco/test-data/genome_results_metaeuk/out.gff3 do a diff on comparison and do produce some lines.

[Hymenium]

Thanks, if this output is working now then that's fine.

[bgruening]

Why was this removed?

We still offer the "download" option in the User Interface.

[abretaud]

Ah found it, it's just the default now. and --offline still works

[bgruening]

I think this is ready to go. I just had one last question. Why do we remove the upload option? I agree that its not a good default, so maybe we should not select this option by default - rather offer the build-in databases, but removing it?

[Hymenium]

The '--update-data' parameter has been removed from BUSCO, see the comments from 15 July.

Strangely this parameter is still mentioned in the user guide (https://busco.ezlab.org/busco_userguide.html#download-and-automated-update).

The user guide says that if a dataset name is provided (using -l or --lineage_dataset) then the associated file is automatically updated, and if a file path is given this is disabled but it seems like a warning will be issued. For automated lineage selection, it says the relevant files are automatically updated .

[abretaud]

Looks good to me, the --update-data is gone but it's just a simplification of options, it doesn't change the wrapper behavior, so I think it's ready

I'm going to merge in a few minutes, unless someone screams ;)

[abretaud]

Ah found it, it's just the default now. and --offline still works