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KarchinLab / open-cravat

A modular annotation tool for genomic variants
MIT License
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scipy is not installed as a requiremnt #272

Open cvaske opened 3 weeks ago

cvaske commented 3 weeks ago

Describe the bug Run ends with error due to a missing scipy import. I'm running a WGS trio from Illumina DRAGEN pipeline through Cravat with ClinVar, case-control, and SpliceAI modules.

To Reproduce In the GUI:

  1. Upload three VCF files.
  2. Select "ClinVar", "SpliceAI", "Gene Ontology" as modules
  3. Upload a case-control cohort in the "Additional Analysis" section.
  4. Start the Annotation

Expected behavior A completed run.

Desktop (please complete the following information):

Run on macOS, using pyenv for a virtual environment based on Python 3.12.1, with no pip installed packages other than open-cravat

Additional context I've attached the run log, and the pip freeze output.

RachelKarchin commented 6 days ago

Hi Charlie! Sorry for the delayed response. We have the scipy installation requirement in our documentation, but per your suggestion we will automate this so that anyone installing the Case-Control Summary module gets a scipy installation if it is not already installed on their machine. This has been added to our job queue and will be out with our next release.