Consolidate execution

[rvhonorato]

The way whiscy is executed by the server backend is:

# Setup
whiscy_setup 1ppe E

# Default
whiscy 1ppe_E.sur 1ppe_E.conv 1ppe_E.phylseq 1ppe_E.out -o 1ppe_E.cons

# Smoothing
whiscy 1ppe_E.lac 1ppe_E.conv 1ppe_E.phylseq 1ppe_E.out -o 1ppe_E.lcons
whiscy_consadjust 1ppe_E.cons -o 1ppe_E.acons
whiscy_resdist 1ppe_E.pdb 1ppe_E.conv 1ppe_E.rd
whiscy_parasmooth 1ppe_E.acons 1ppe_E.lcons 1ppe_E.rd -o 1ppe_E.pscons
whiscy_haddock 1ppe_E.pdb 1ppe_E_haddock.pdb 1ppe_E.pscons

This can be refactored into

# Run default prediction
$ whiscy 1ppe E 

# Run full prediction -> consadjust + resdist + parasmooth + haddock
$ whiscy 1ppe E --full

Then we can remove whiscy_setup entirely and integrate its steps.

Also I see that the intermediate CLIs are only used in this full prediction - I see no other mention of those.

If they are not useful by themselves, them they can also be absorbed into the whiscy CLI - could you confirm @amjjbonvin ?