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LUMC / HAMLET

RNA-seq pipeline for AML diagnostics developed in collaboration with the LUMC Hematology department
MIT License
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Problem detecting Singularity #12

Closed rschauner closed 3 years ago

rschauner commented 3 years ago

I activated the conda enviorment and built singulairty from the GitHub on MacOS 10.15.7 successfully.

Output from singularity version: 3.7.3+125-g9434baf17

When I run the first test (pytest --kwd --tag sanity), it fails because the output does not contain "singularity version 3." Keeping the output this is one of the files.

cat /var/folders/fn/0ljsn56d78dbw6nlm5ly7fbxtm2f76/T/pytest_workflow_5jbmvtid/test-qc-sanity-singularity/log.out
singularity-ce version 3.7.3+125-g9434baf17

Is there any recommendation for solving this? It seems like its just a testing issue, but I don't know if there is something different with this version of singularity.

Redmar-van-den-Berg commented 3 years ago

I've made an update to the code checking the singularity version here, can you give this branch a try?

I don't expect any issues using that version of singularity, although HAMLET hasn't been tested on MacOS at all, so I'll be interested to know how it works for you.

rschauner commented 3 years ago

Just tried using the issue-12 branch to run the tests. All of the tests up to the functional test passed. I'm trying to download the test data to run the rest of the tests, but it very large.

Redmar-van-den-Berg commented 3 years ago

Thanks for checking this fix, I've merged the changes.

The tests data itself is actually part of HAMLET and quite small, but the reference files that HAMLET uses are indeed very large (100+GB, since they include the human reference genome indexed for many different tools).