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usegalaxy-no / galaxyadmin

A repository for managing the work of the usegalaxy.no GalaxyAdmin team
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miRNA workflow fails #35

Closed ehj000 closed 3 years ago

ehj000 commented 3 years ago

The most recent version of miRNA differential expression (miRBase, hg38) is failing with the following error: Traceback (most recent call last): File "_evaluateexpression.py", line 1, in from galaxy_ext.expressions.handle_job import run; run() File "/srv/galaxy/server/lib/galaxy_ext/expressions/handle_job.py", line 21, in from galaxy.tools.expressions import evaluate File "/srv/galaxy/server/lib/galaxy/tools/init.py", line 60, in from galaxy.tools.cache import ToolDocumentCache File "/srv/galaxy/server/lib/galaxy/tools/cache.py", line 15, in from sqlitedict import SqliteDict ModuleNotFoundError: No module named 'sqlitedict'

kjetilkl commented 3 years ago

This is clearly a dependency issue. We had similar problems with this tool in October, but Torfinn managed to fix them.

torfinnnome commented 3 years ago

@ehj000 Can you share a failing history with me? torfn@nmbu.no on usegalaxy.no.

ehj000 commented 3 years ago

I have shared it earlier: https://usegalaxy.no/u/bf52c02868d747c5b784466753839ed6/h/rt15023 Copying the files to test now and will share that history as well when done

torfinnnome commented 3 years ago

Fixed: https://github.com/usegalaxy-no/infrastructure-playbook/commit/6f950779235de903b4216fbdc37f363daf2a8f46

Should work now?

ehj000 commented 3 years ago

I am not able to evaluate the results, but the workflow is completing now. Thanks