Make hardier

[schorlton]

I suppose it's a bit hard to see the diffs as Github doesn't account for moved files, but in summary:

1. Set -euo pipefail to make it fail when a subcommand fails or if undefined variables
2. Add flag to run BLAST analysis
3. Expect all tools to be in PATH. A user should symlink them into PATH or change the script if not so.
4. Define variables with their defaults as was previous set.
5. Bump version

Thanks for your consideration!

[SAMtoBAM]

Hi there,
Sorry for the late reply.
I think 'make hardier' is the appropriate title, it has been something in the back of my head for a bit now
So taking your nudge I am rewriting somethings to make it easier to use.
Due to the branch conflicts and other things I was adding in the mean time, I will just add a new version of MUM&Co (3.8) soon separately.

1. I will add this as you suggested.
2. I will add the blast option
3. Agreed, were you specifically referring to the BLAST step?
4. I am adding defined defaults

On top of this it will now check to see if all the variables are set and warn you and exit if they are found to be empty etc.

Thanks for the suggestions

[SAMtoBAM]

Added v3.8 now which should be much more hardier
Thanks again