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wodanaz / Assembling_viruses

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pangolin from conda version causing issues. #82

Closed wodanaz closed 2 years ago

wodanaz commented 2 years ago

Hi John, I may need some help with pangolin. They made a major upgrade and I am having similar issues to the ones we had with the last major upgrade. The conda version doesn't appear to be installing well with the new variant data.

I have been able to get a previous version (i.e. v 3.1.17) to the upgrade (v4.0.4) to work using pangolin outside the pipeline but when I run the regular pipeline it fails in both Azure and Hardac.

This is not a priority because I think I can report what I have.

I am using hardac for the data I got today because It was delivered via sftp

Thanks John and have a good weekend

johnbradley commented 2 years ago

@wodanaz Is this error you are seeing in logs/run_pangolin.log ?

Error: please install `pangolin_data` with 
pip install git+https://github.com/cov-lineages/pangolin-data.git
wodanaz commented 2 years ago

Yes it is related to that 😊

johnbradley commented 2 years ago

The pangolin step environment installs the latest version of pangolin: https://github.com/wodanaz/Assembling_viruses/blob/12dbd307bea761b0ba6ea0d9a750eb3d5af491a7/workflow/envs/pangolin.yml#L6 So just re-installing it might fix your problem. Have you tried deleting your conda cache directory SM_CONDA_PREFIX and re-running the workflow? Snakemake would have to install pangolin from scratch and hopefully include everything needed.

If that doesn't work try updating the - pangolin line in pangolin.yaml to:

- pangolin=4.0.4

Version 4.0.4 is the latest version of bioconda/pangolin right now.

wodanaz commented 2 years ago

No I haven't try this but will do in a sec. Sorry for my delay.

wodanaz commented 2 years ago

Yes, removing the cache fixed the issue. Thanks so much John!