Question: Python modules not found when running job
gravatar for jeroen.galle
24 months ago by
jeroen.galle30 wrote:

Hi I'm reinstalling my galaxy server to start with supervisord and pass jobs trough slurm. Now my galaxy is running with an admin account and i can log in but when i test the jobs by pasting some text in data upload the job immediately goes to failed state and gives the following error:

Traceback (most recent call last):
  File "/srv/galaxy/server/tools/data_source/", line 18, in <module>
    from galaxy.datatypes import sniff
  File "/srv/galaxy/server/lib/galaxy/datatypes/", line 22, in <module>
    from galaxy.datatypes.binary import Binary
  File "/srv/galaxy/server/lib/galaxy/datatypes/", line 13, in <module>
    import pysam
ImportError: No module named pysam
Traceback (most recent call last):
  File "/srv/galaxy/server/database/jobs/000/16/", line 1, in <module>
    from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()
  File "/srv/galaxy/server/lib/galaxy_ext/metadata/", line 23, in <module>
    from sqlalchemy.orm import clear_mappers
ImportError: No module named sqlalchemy.orm

My supervisor galaxy.conf is:

command         = uwsgi --plugin python --virtualenv /srv/galaxy/server/.venv --ini-paste /srv/galaxy/server/config/galaxy.ini
directory       = /srv/galaxy/server
autostart       = true
autorestart     = true
startsecs       = 10
user            = galaxy
stopsignal      = INT

command         = python ./scripts/galaxy-main -c /srv/galaxy/server/config/galaxy.ini --server-name=handler%(process_num)s
directory       = /srv/galaxy/server
process_name    = handler%(process_num)s
numprocs        = 2
umask           = 022
autostart       = true
autorestart     = true
startsecs       = 10
user            = galaxy
environment     = VIRTUAL_ENV="/srv/galaxy/server/.venv",PATH="/srv/galaxy/server/.venv/bin:%(ENV_PATH)s",DRMAA_LIBRARY_PATH="/usr/lib/slurm-drmaa/lib/"
stdout_logfile  = /srv/galaxy/server/handler%(process_num)s.log
redirect_stderr = true

programs = galaxy,handler

Any ideas?

Thanks in advance!


installation supervisord venv • 1.6k views
ADD COMMENTlink written 24 months ago by jeroen.galle30
gravatar for david.a.morais
23 months ago by
david.a.morais110 wrote:

I had a similar problem with the upload tool

I posted the answer here:

I hope this helps you


ADD COMMENTlink written 23 months ago by david.a.morais110
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