On 21/02/2011 16:20, Nate Coraor wrote:
Marina Gourtovaia wrote:

In a bash shell, I define the path (needed both by Galaxy to find
the right version of python and by tools that run on a cluster to
find the executables) and some other  global variables on the
command line. The cluster jobs (LSF) inherit all these values. This
is my line

PATH=/usr/bin:/software/solexa/bin:$PATH  http_proxy="http://somecache:3128"; sh 

Is there anything inherently wrong with this simple solution?
No, this is effectively what we do to start the server.  The only
difference is that when using PBS the environment is not passed through
to the cluster.  Is that a feature specific to LSF?


This is a feature of LSF, a very useful one. An LSF job inherits the environment of the user who started it and knows where the home directory of this user is. We run our pipelines as a special user, and I am going to run the production Galaxy server as another special user.

I do not know whether LSF is configured like this at Sanger or this is is generic feature


The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. _______________________________________________
To manage your subscriptions to this and other Galaxy lists, please use the 
interface at:


Reply via email to