generalizing the PBS submission script example by using environment variables to specify certain locations

#!/bin/bash
# MOAB/Torque submission script for SciNet GPC
#
#PBS -l nodes=1:ppn=16,walltime=10:00:00
#PBS -N RACS_ORF_run -q largemem

# load modules, ie. to use, eg. SamTools and BWA
module load samtools/1.3.1 bwakit


# define some environment variables to generalize the submission script
# RACS location
RACS=PATHtoRACS
# INPUT and IP files location
DATA=PAHTtoDATA
# REFerence files, eg. gff3 and fasta for T.T.
REFS=PATHtoREFS

# location of RAMDISK, typically /dev/shm or /tmp
RAMDISK=/dev/shm


# DIRECTORY TO RUN - $PBS_O_WORKDIR is directory job was submitted from
cd $PBS_O_WORKDIR

# EXECUTION COMMAND
# RACS repo located on $SCRATCH
# data subdirectory containing data files: INPUT and IP files
# refs subdirectory containing reference files: fasta and gff3 files
# the pipeline will attempt to use RAMDisk (/dev/shm) and autodetect maximum number of cores to use
($RACS/core/countReads.sh        \
        $DATA/SSCH1-1_Input_S2_R1_001.fastq.gz  $DATA/SSCH1-1_ChIP_S1_R1_001.fastq.gz       \
        $REFS/T_thermophila_June2014_assembly.fasta  $REFS/T_thermophila_June2014.gff3  $RAMDISK  \
        >& output.log) &

wait