Create inchworm.sh

first stage of Trinity
Create chrysalis.sh

Second stage of Trinity. Should use local network disk
Create butterfly.sh

Last stage of Trinity. I/O heavy; needs local disk access. 
This stage can be properly parallelised, but needs significant changes to NGSane core software architechture
Output Bug

line 59 needs to be checked/changed to ensure proper output directory and not qsub log/output file
Create trinity_config.txt

A bit messy.
Update trigger.sh
Update trigger.sh
Update butterfly.sh
first commit
can i only commit a few files?
modified job jubmission and preparejob submission. Ready for beta testing
changed header.sh
permissions changed
debugged inchworm.sh.. stupid keybord
debugged jobsubmission... someone sneaky changed the job name nomenclature rules
made chrysalis faster by copying files to local hard disk
ironed out a few bugs.
Tidy-uped the trigger...
Preparing QC and HTML output
Fixed local disk parameters for chrsalis