#!/bin/bash
#$ -S /bin/bash                                             # Use a real BASH shell on the worker node
#$ -q ${queues}                                             # What queues do you want to submit to
#$ -M ${email_addy}                                         # Send email updates to this address
#$ -m beas                                                  # When to send an email update
#$ -e /data/users/dunnw/logs/${call_id}.e                   # Write standard error to this file
#$ -o /data/users/dunnw/logs/${call_id}.o                   # Write standard out to this file
#$ -N ${job_name}                                           # Name my job this
#$ -R y                                                     # Reserve cores for me until there are the number I asked for
#$ -pe openmp ${core_range}                                 # Use openmp for multiprocessor use and give me core_range cores

LD_LIBRARY_PATH="${ld_library_path}$${}{LD_LIBRARY_PATH}"   # Make sure worker's LD_LIBRARY_PATH contains ld_library_path


# HPC clusters frequently use a module system to provide system wide access to 
# certain programs.  The following makes sure that the tools needed are loaded
# for **MY** cluster. You will need alter this to make sure your cluster is set up
# based on its system.

module load bowtie2/2.0.2
module load tophat/2.0.6
module load cufflinks/2.0.2
module load samtools/0.1.18


# basic staging stuff
DATAHOME="${datahome}"
MYSCRATCH="/scratch/$${}{USER}"


mkdir -p $MYSCRATCH
cd $MYSCRATCH


# Remind me what will be done
echo ''
echo "${cmd_str}"
echo ''

# Run my job
${cmd_str}


# Pack up results and send it home to log-in node
tar -zcvf ${call_id}.tar.gz ${out_dir}
cp ${call_id}.tar.gz $${}{DATAHOME}/

# Back into the shadows
cd $HOME
rm -rf $MYSCRATCH