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@itsc.uni-luebeck.de www.itsc.uni-luebeck.de Am Dienstag, den 27.06.2017, 12:54 +0100 schrieb Maximilian Friedersdorff:
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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