I followed the advice for multiple installed python versions to set ~galaxy/galaxy-python/python and set the environment for the galaxy user to have that in the PATH
Problem is, when a job is started on GridEngine, it does not use the "-V" flag to inherit the environment. So it runs with a different python version and more important it does not set LD_LIBRARY_PATH and fails for some tools which need some special lib. (libRblas in this case) Where can I fix that?
You should be able to set it in your shell's startup files (like ~/.bash_profile).
It is set in ~/.bashrc, which is source by ~/.bash_profile. If I normally login to a cluster node via ssh it is set correctly. But if I qsub a job, it is not read. Except when I set the "-V" switch. So I either need to change gridengines behaviour or make galaxy use that switch.
Is there a easy way to config how to submit cluster jobs?