Question: Python modules not found when running job
0
jeroen.galle • 30 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/upload.py", line 18, in <module>
from galaxy.datatypes import sniff
File "/srv/galaxy/server/lib/galaxy/datatypes/sniff.py", line 22, in <module>
from galaxy.datatypes.binary import Binary
File "/srv/galaxy/server/lib/galaxy/datatypes/binary.py", line 13, in <module>
import pysam
ImportError: No module named pysam
Traceback (most recent call last):
File "/srv/galaxy/server/database/jobs/000/16/set_metadata_ulI5bX.py", line 1, in <module>
from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()
File "/srv/galaxy/server/lib/galaxy_ext/metadata/set_metadata.py", line 23, in <module>
from sqlalchemy.orm import clear_mappers
ImportError: No module named sqlalchemy.orm
My supervisor galaxy.conf is:
[program:galaxy]
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
[program:handler]
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/libdrmaa.so.1"
stdout_logfile = /srv/galaxy/server/handler%(process_num)s.log
redirect_stderr = true
[group:gx]
programs = galaxy,handler
Any ideas?
Thanks in advance!
Jeroen
