Thanks for your help, Marius.
Turns out what I need is this:
<destination id="uge_default" runner="uge">
<env id="GALAXY_VIRTUAL_ENV">None</env>
</destination>
Otherwise the job script that is written by Galaxy will activate the
virtual env on the worker node, which is not what I want to happen.
Cheers
Ulf
On 25/10/17 17:27, Marius van den Beek wrote:
Are you perhaps using a supervisor setup where you are setting the PATH ?
In that case you can
remove /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/.venv/bin from
the PATH.
If you're referencing python you can directly use the path
to /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/.venv/bin/python.
Best,
Marius
On 25 October 2017 at 18:24, Ulf Schaefer <[email protected]
<mailto:[email protected]>> wrote:
Hi Marius
This is very useful, but not quite there.
I use in my job_conf.xml
<destination id="uge_default" runner="uge">
<env id="PATH">/this/is/a/test</env>
</destination>
and I end up with this
PATH=/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/.venv/bin:/this/is/a/test
Any idea where that came from?
Thanks
Ulf
On 25/10/17 16:05, Marius van den Beek wrote:
Hi Ulf,
you can set a virtualenv to be used in your job_conf.xml file.
The following line would go into the
`<destination></destination>` tag:
`<env file="path_to_venv/bin/activate" />`
Best,
Marius
On 25 October 2017 at 16:56, Ulf Schaefer
<[email protected] <mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>> wrote:
Hi again
Update, sorry for spamming:
It is not ALL jobs that fail. Only the ones that get
dispatched to
our Grid Engine cluster (so nearly all).
The reason appears to be that the path to the Python binary
is added
to the PATH variable when the job arrives on the worker node:
[galaxy_hpc@hpc1node25 galaxy-dist]$ export
PATH=/home/galaxy_hpc/galaxy-dist/.venv/bin:/tmp/5000354.1.researchmid.q:/usr/local/bin:/bin:/usr/bin
[galaxy_hpc@hpc1node25 galaxy-dist]$ python
Could not find platform dependent libraries <exec_prefix>
Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
Python 2.7.6 (default, Oct 25 2017, 12:28:23)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] on linux2
Type "help", "copyright", "credits" or "license" for more
information.
>>> import json
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named json
This is the wrong python to be running there. It should just
go with
the one in /usr/bin. If I change PATH, it works fine:
[galaxy_hpc@hpc1node25 galaxy-dist]$ export
PATH=/tmp/5000354.1.researchmid.q:/usr/local/bin:/bin:/usr/bin[galaxy_hpc@hpc1node25
galaxy-dist]$ python
Python 2.6.6 (r266:84292, Aug 9 2016, 06:11:56)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-17)] on linux2
Type "help", "copyright", "credits" or "license" for more
information.
>>> import json
>>>
Does anyone have an idea how I can stop this from happening?
Where
is the PATH set before submitting the job?
Thanks
Ulf
On 25/10/17 15:23, Ulf Schaefer wrote:
Hi all
After running the recommended update I am now on branch
17.09.
As part
of the update I set up a new virtual env running an
additional
python
2.7.6. My previous virtual env was running 2.6.6 which
is a system
requirement for Centos 6.
All dependencies were installed and Galaxy starts fine,
but no tools
run. The error is always a variation of this:
Could not find platform dependent libraries <exec_prefix>
Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
Traceback (most recent call last):
File
"galaxy-dist/database/jobs_directory/000/418/418014/set_metadata_4LcsZv.py",
line 1, in <module>
from galaxy_ext.metadata.set_metadata import
set_metadata;
set_metadata()
File
"galaxy-dist/lib/galaxy_ext/metadata/set_metadata.py",
line 19,
in <module>
import json
ImportError: No module named json
I put some debug output at the top of set_metadata.py
and it is
indeed
running the correct python version from the virtual env.
Needless to say
I can import json just fine using that python version.
Any ideas?
Any help is greatly appreciated.
Thanks
Ulf
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