Re: [galaxy-dev] Metadata setting python dependencies

Thanks for your help, Marius. Turns out what I need is this: None 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

Re: [galaxy-dev] Metadata setting python dependencies

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

Re: [galaxy-dev] Metadata setting python dependencies

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:

Re: [galaxy-dev] Metadata setting python dependencies

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

Re: [galaxy-dev] Metadata setting python dependencies

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: