Hi,
i ran into that too (on debian 8). I'm not that familiar with virtual environments but
this is what I found out.
It looks like the virtual environment doesn't get activated properly in the shipped
ini.d-file (it is the shipped one, right?).
If I add ". /path/to/.venv/bin/activate" to it, everything runs just fine.
"run.sh" has this line. The init.d-file hasn't. It just calls the .venv-
python directly. It seems like that's not fully equivalent to activating .venv and
running python in there. I don't really know why. I'm guessing
PATH-magic.
Hope that helps a bit.
Gudrun Amedick
--
Gudrun Amedick
IT-Systemtechnik
UNIVERSITÄT ZU LÜBECK
IT-Service-Center
Ratzeburger Allee 160
23562 Lübeck
Tel +49 451 3101 2035
Fax +49 451 3101 2004
amedick(a)itsc.uni-luebeck.de
Hi All,
when my local galaxy is started using the init system (systemd on Ubuntu
16.04 in this instance). Some tools will fail, indicating that some
python module do not exist. This is the result of uploading a 2KB plain
text file:
Traceback (most recent call last):
File "/home/galaxy/galaxy/tools/data_source/upload.py", line 20, in
<module>
from galaxy.datatypes import sniff
File "/home/galaxy/galaxy/lib/galaxy/datatypes/sniff.py", line 31, in
<module>
from galaxy.datatypes.binary import Binary
File "/home/galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 14, in
<module>
import pysam
ImportError: No module named pysam
Traceback (most recent call last):
File
"/home/galaxy/galaxy/database/jobs_directory/000/39/set_metadata_EI05GD.py",
line 1, in <module>
from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()
File "/home/galaxy/galaxy/lib/galaxy_ext/metadata/set_metadata.py", line 23,
in <module>
from sqlalchemy.orm import clear_mappers
ImportError: No module named sqlalchemy.orm
When the same galaxy install is started directly using the 'run.sh'
script in the install directory, everything works fine.
I've verified that I can manually import pysam and sqlalchemy.orm if I
execute the python interpreter located at <install_dir>/.venv/bin/python
directly.
Any ideas?
I've attached the init script.
TL;DR
Galaxy cannot import some python modules when started by the init
system. No idea why.
Galaxy version: 17.05
OS: Ubuntu 16.04
Many Thanks
Max
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