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/pyt
Hi Marius
This is very useful, but not quite there.
I use in my job_conf.xml
/this/is/a/test
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 `` tag:
``
Best,
Marius
On 25 October 2017 at 16:56, Ulf Schaefer wrote:
> Hi again
>
> Update, sorry for spamming:
>
> It is not ALL jobs that fail. Only the ones that get dispatched t
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@hp
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 f