tbl2asn is expired about bacass

[apeltzer]

A version of tbl2asn without timeout is coming soon 🎉 - once we have that upstream available, I'll make a re-release of the pipleine to make things 100% reproducible (even after 6 months!) :-)

[zdk123]

We're having issues with tbl2asn-forever on nextflow. Might be related to audy/tbl2asn-forever#2

[apeltzer]

Yeah I might just wait until tbl2asn (the original one) is updated and then give it a go 👍

[apeltzer]

Which container?

I already tried actively pursuing the author of prokka here tseemann/prokka#444 but there is not really a solution. For the sake of reproducibility, its also not really an option to "redo" the container every 6months. The alternative annotation tool shipped with 1.1.0 of the pipeline should however be usable nevertheless ...?

Sorry, this is more of an upstream issue & there is not really a fix until this was fixed either in tbl2asn or prokka drops usage of this method/tool....

[zdk123]

I am using nfcore/bacass:1.1.0. I see that this is an ongoing issue for prokka/tbl2asn users, thanks for pointing that out.

In another container we're building ourselves, grabbing the newer binary from the ftp site worked well enough. I'll try dfast too and see if those results are acceptable, thanks!

[apeltzer]

Yes, sorry that there isn't a "proper" solution as of now - the other thread in Prokka also links to bioconda where people were discussing potential solutions to resolve that problem. Can't really "fix" it in here 👎

[angelovangel]

Dear @apeltzer,
I agree that it is critical to maintain reproducibility, and redoing the container every 6 months is not a solution. On the other hand, -profile test,docker automatically failing because of this issue is also not an option, right? Currently it fails, I will make a PR to include a test_dfast profile (using dfast instead of prokka) for the time being, you cold consider making this the default test profile in the future in case the issue is not resolved otherwise.

Best,
Angel

[angelovangel]

That’s great, it was a never-ending headache for many.

[apeltzer]

That one could also help: bioconda/bioconda-recipes#20073

[zdk123]

will test this today, thanks!

[apeltzer]

Just keep in mind that the newest version of tbl2asn will not have the timeout thing anymore. I guess it will just take some time to have this updated on bioconda, then these issues will go away hopefully forever ;-)