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fmalmeida / bacannot

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
https://bacannot.readthedocs.io/en/latest/
GNU General Public License v3.0
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Upgrade Bakta to 1.5.1+ #75

Closed sunitj closed 1 year ago

sunitj commented 1 year ago

Is your feature request related to a problem? Please describe. Pipeline currently uses v1.5.0 of Bakta. This version suffered from a bug causing Diamond runtime errors during the pseudogene detection step.

Describe the solution you'd like Please consider upgrading to version 1.5.1 or 1.6.0.

Additional context Bakta Releases

fmalmeida commented 1 year ago

Hi @sunitj , Thank you for pointing that out. I will work on that to try to have it ASAP.

fmalmeida commented 1 year ago

Hi @sunitj ,

I have already updated the tool to v1.6.0 and tested it in branch 75-upgrade-bakta-to-151+.

If you already need it, you can try to execute the pipeline using this specific branch. To generate a release from it I still need to address some small cleanups and info updates in the manuals. Also, I am planning to add a parameter to allow users to easily select different versions of the tool.

So, an actual release merged to master I think I will have only by Monday. But, you can already use it from the newly generated branch 😄

Thank you for pointing this issue out 🚀

sunitj commented 1 year ago

Thank you for the swift patch! Really appreciate all the work you and your team have put into this package. Closing this issue.

fmalmeida commented 1 year ago

Hi @sunitj , Glad to hear that it's working good 😄 I will re-open the ticket to close is when I merge it to master (which should happen very soon) just so I don't loose track of it. Hope you enjoy using the tool.