Skip to content
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.

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

Install PGAP #1011

Closed
wants to merge 1 commit into from
Closed

Install PGAP #1011

wants to merge 1 commit into from

Conversation

neoformit
Copy link
Collaborator

It's a pipeline - PGAP tool is included as folder instead of Conda package:
https://toolshed.g2.bx.psu.edu/repository?repository_id=b0fc108867dbc651&changeset_revision=e0c913351502

If it works, and we can't offer an alternative (NCBI-ready ouput), I don't see why we shouldn't provide the user with the functionality? PGAP is made by NCBI so it seems reasonable for us to have it on GA.

Ticket: https://support.ehelp.edu.au/a/tickets/107774

image

@neoformit neoformit requested review from cat-bro and mthang December 27, 2023 19:47
@neoformit
Copy link
Collaborator Author

@cat-bro

If we can avoid installing this (Igor suggested Prokka as an alternative) that would be good because it has what looks like a difficult combination of conda packages, and no tests

I agree it looks like it sucks, but it is pretty popular on GitHub. If we install and it's broken, we can just take it down?

@neoformit
Copy link
Collaborator Author

The user has requested PGAP - "Prokaryotic Genome Annotation Pipeline": https://github.com/ncbi/pgap.
But the toolshed link that Igor found is PGAP - "Pan-Genome Analysis Pipeline": https://sourceforge.net/projects/pgap/

@neoformit neoformit closed this Jan 15, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

1 participant