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.

Sign up for GitHub

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

Jump to bottom

Fix #237: Upgrade Skesa container to 2.5.1 to fix ownership issue with /tmp #240

Merged
merged 2 commits into from
Feb 9, 2024
Merged

Fix #237: Upgrade Skesa container to 2.5.1 to fix ownership issue with /tmp #240

merged 2 commits into from
Feb 9, 2024

Conversation

samuell
Copy link
Contributor

@samuell samuell commented Dec 13, 2023 •
edited
Loading

Description

See #237

This PR fixes #237 by upgrading the Skesa container to version 2.5.1.

Primary function of PR

  • Hotfix
  • Minor functionality improvement
  • Major functionality improvement / New type of analysis
  • Backward-breaking functionality

Testing

Sign-offs

@samuell samuell changed the title Fix #237: Upgrade Skesa to 2.5.1 to fix ownership issue with /tmp Fix #237: Upgrade Skesa container to 2.5.1 to fix ownership issue with /tmp Dec 13, 2023
@samuell samuell marked this pull request as ready for review December 13, 2023 19:55
@samuell samuell requested a review from sylvinite as a code owner December 13, 2023 19:55
@samuell
Copy link
Contributor Author

samuell commented Dec 14, 2023 •
edited
Loading

Just noting this conversation from Slack:

Ryan James Kennedy 6 hours ago
We need test samples for all the species we run to check that updates of software work across the board. Is that possible to organise @ Isak Sylvin

Isak Sylvin 6 hours ago
Sitting in another meet so bit distracted.
But yea it shouldnt be hard to organise. Could just saw down existing MRSA samples to mini dataset. Could even share it publicly on github at that point

@ryanjameskennedy
Copy link
Collaborator

@mhkc where did you find those test reads for tb? Or did you just simulate reads from the reference genome? (wgsim is a good tool for this btw)?

@mhkc
Copy link
Collaborator

mhkc commented Jan 17, 2024 •
edited
Loading

I just took public samples from EBI with annotated as being antibiotic resistant and with good sequencing depth.

@samuell
Copy link
Contributor Author

samuell commented Feb 1, 2024 •
edited
Loading

Have been testing now on some resistant Klebsiella data:

The following are correctly typed as carbapenem resistant by both resfinder and amrfinder:

The following is resistant according to amrfinder, susceptible according to resfinder:

These strains are supposed to be colistin resistant (according to description), but is only typed as susceptible by resfinder (no colistin from amrfinder):

These are supposed to be meropenem resistant, but only typed as susceptible by resfinder (no typing by amrfinder):

Supposed to be resistant to silver nanoformulations, typed as silver resistant by amrfinder:

Any comments on this @mhkc @ryanjameskennedy ? Is this testing procedure sufficient, and are the results acceptable? Otherwise, do you have suggestions for other things to try?

@samuell samuell merged commit 539d8ab into master Feb 9, 2024
1 check passed
@samuell samuell deleted the 237-upgrade-skesa branch February 9, 2024 10:03
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@sylvinite sylvinite sylvinite approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Can not bind to sub-folders of /tmp in skesa container
4 participants
@samuell @ryanjameskennedy @mhkc @sylvinite