adding masurca version 4.1.2 #908
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kapsakcj
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May 3, 2024
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thanks for adding all these relative links 👍
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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 |
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OK tests look happier now that |
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Something about not able to set mempolicy and interleave mask: I'm not sure what to do here.... |
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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 |
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I am encountering problems with the biocontainer image as well (quay.io/biocontainers/masurca:4.1.1--pl5321hb5bd705_0): So... hmm... |
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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. |
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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 |
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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. |
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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)