Several MAF-related tools fail with the same error message

usegalaxy-no / galaxyadmin

A repository for managing the work of the usegalaxy.no GalaxyAdmin team

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Several MAF-related tools fail with the same error message #89

Closed kjetilkl closed 1 year ago

kjetilkl commented 1 year ago

On April 2, a user tried to run several MAF-related tools ("MAF to FASTA", "MAF to Interval" and "Extract MAF by block number") that all failed with the same error message:

File "/srv/galaxy/server/lib/galaxy/model/__init__.py", line 72, in 
    from sqlalchemy.orm import (
ImportError: cannot import name 'registry'

kjetilkl commented 1 year ago

These tools are all internal tools (located in /srv/galaxy/server/tools/maf/) and they don't specify any requirements, which means that they are executed with the default Singularity container. I suspect that the error could be caused by different versions of the SQLAlchemy package being used by the container (v1.3.24) and Galaxy 21.09 (v1.4.20). If so, there may be other tools running with the default container that are affected by related issues as well.

kjetilkl commented 1 year ago

I updated the default container to use "sqlalchemy==1.4.20", and that solved the problem!