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#
# MATLAB MRC runtime environment script for Nordugrid ARC
#
# Runtime environment scripts are called (bash source)
# from NorduGrid ARC with argument 0,1 or 2.
# First call with argument "0" is made before the the batch
# job submission script is written on the frontend.
# Second call is made with argument "1" just prior to execution of the
# user specified executable on the node.
# Third "clean-up" call is made with argument "2" after the user
# specified executable has returned on the node.
#
# author: Kimmo Mattila <Kimmo.Mattila@csc.fi>
# updated: 2012-10-01
#
# shared directory for application installation 
application_base_path=/cvmfs/fgi.csc.fi/apps/sl6

# number of threads for execution
case "$1" in
0 )
# Here we can reserve a whole node (with $num_threads cores) for running BWA threaded.
# This can be done for example by reserving memory worth of one node, if no
# more elegant ways are available.
# We set the number of threads and check that the user has specified 
# the thread count option in the script and is able to take advantage of
# multiple thread reservation.

;;
1 )
# set MCR directory
export MCRROOT=$application_base_path/matlab/v717
;;
2 )
# If you need to create the temporary directory manually instead of LRMS
# this is the place to clean it up.
;;
* )
# Now, calling argument is wrong or missing.
# If call was made from NorduGrid ARC, it is considered
# an error.
return 1
;;
esac
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