[galaxy-user] setting environment for sge scripts

[Nate Coraor]

Andreas Kuntzagk wrote:

> 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?

Andreas,

You should be able to set it in your shell's startup files (like 
~/.bash_profile).

--nate