#
# SAMTOOLS 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.
#
#

# shared directory for application installation 
application_base_path=/v/linux26_x86_64/appl/molbio

# 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  SAMTOOLS  directory
    export SAMTOOLS_DIR=$application_base_path/samtools/samtools-0.1.18/bin

    # set path to the SAMTOOLS binaries
    export PATH=$PATH:$SAMTOOLS_DIR/
    
;;

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