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
amed...@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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