Conversation
kapsakcj
reviewed
May 3, 2024
Collaborator
There was a problem hiding this comment.
thanks for adding all these relative links 👍
Collaborator
|
I see some errors in the test command at the end, I'm surprised it exited 0 and the image built successfully. Looks like it requires maybe try adding |
Collaborator
|
OK tests look happier now that |
Collaborator
|
Something about not able to set mempolicy and interleave mask: I'm not sure what to do here.... |
Contributor
Author
|
From what I gather, it looks like Docker prevented numactl from setting mempolicy. https://forums.docker.com/t/cannot-run-numactl-interleave-all-in-docker/40631/5 |
Contributor
Author
|
I am encountering problems with the biocontainer image as well (quay.io/biocontainers/masurca:4.1.1--pl5321hb5bd705_0): So... hmm... |
Contributor
Author
|
I'm a little torn about what to do with this one.
I need to read up on the new GRID_ENGINE=MANUAL to see if that can fix things. I'll move this to a draft for now. |
Collaborator
|
I wouldn't burn too much time/effort on this if you are utilizing POLCA in other ways. If someone really wants to use masurca for hybrid assembly via a docker image, then we can ask them to help with resolving these issues. I don't work with this tool ever so it's difficult for me to troubleshoot |
Contributor
Author
|
For completeness, I checkout out version 4.1.2 today, and issue remains: This issue is a problem with running masurca with docker. I may try building the image and running with singularity, but not today. |
Contributor
Author
|
This PR was too difficult to update due to too many out-date file changes, so I created a new branch with a new PR here #1359 (This new masurca version still doesn't work) |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
There's a new version of MASURCA! (More info here: https://github.com/alekseyzimin/masurca/releases/tag/v4.1.1)
I copied the files from 4.1.0 and made the following changes:
Pull Request (PR) checklist:
docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15)spades/3.12.0/Dockerfile)shigatyper/2.0.1/test.sh)spades/3.12.0/README.md)