On 21/02/2011 16:20, Nate Coraor wrote:
Marina Gourtovaia wrote:
Hi
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
DRMAA_LIBRARY_PATH=/usr/local/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.4
PATH=/usr/bin:/software/solexa/bin:$PATH http_proxy="http://somecache:3128"; sh
run.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?
--nate
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
Marina
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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.
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