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McIntosh-Lab / tvb-ukbb

TVB-UKBB Pipeline: TheVirtualBrain implementation of the UK Biobank pipeline
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bash sometimes overlooks conda environment's python installation when running script #7

Closed noahfl closed 4 years ago

noahfl commented 4 years ago

The common error seen when this issue arises is

Traceback (most recent call last):
  File "/liberatrix/mcintosh_lab/ukbb/UK_biobank_pipeline_v_1/bb_pipeline_tools/bb_pipeline.py", line 31, in <module>
    from bb_file_manager import bb_file_manager
  File "/liberatrix/mcintosh_lab/ukbb/UK_biobank_pipeline_v_1/bb_pipeline_tools/bb_file_manager.py", line 29, in <module>
    import nibabel as nib
ModuleNotFoundError: No module named 'nibabel'

The current fix is to run

conda deactivate conda activate /liberatrix/mcintosh_lab/[user dir if applicable]/ukbb/software/env

and then it'll run normally.

noahfl commented 4 years ago

Seems like there's no real fix for this since it seems to happen arbitrarily. I think the best option at this point is to just add something in the documentation about how to refresh the environment if it does happen.

noahfl commented 4 years ago

Seems to have resolved itself in recent iterations of the environment. Closing