Remove ulimit config from script
Remove manual logging from script.

Uses SGE logs instead
Rename helpers and create SGE log directories
deleted a space
fixed an error with pdg to png line
renamed path to inotifywait
moved log directories creation to parent script
Repository for old code.
Recursively finds all pdf and convert them to png
Rewrote makefile generator to use SGE to dispatch jobs
Wrapper for running bcl2fastq using SGE
Wrapper to run coverage stats using SGE
SGE script for bcl2fastq
Code and list of files to keep and delete during cleanup
SGE script for running coverage stats
SGE script for running BWA alignment
SGE script for running GATK preprocess
SGE script for running GATK genotyper
SGE Script for running GATK recal
SGE Script for running SAM merge