This comprises two changes the most important of which is in commit 227748f3 which adds support for the new fsl_sub. As the new fsl_sub shell backend (e.g. no cluster) can parallelise over available cores I have removed all SGE checks. The (redundant) selection of -q long.q has been removed as this won't work at BMRC Now using --coprocessor=cuda to select a GPU queue
Second merge request is suggestions to improve security of the script by quoting variables when arguments to external commands. This avoids issues with users providing 'something; rm -rf /'). = '', ! = '' and x"" = x is all very old syntax - use -z and -n for empty and non-empty strings instead.
You could also consider replacing `` with $() which is modern shell syntax but this hasn't been done here as I didn't want to mask the other changes.
I decided not to quote "$FSLDIR/acommand" but this would be a wise change.