Changes to determine optimal partitioning.
(Also includes broad refactoring of the code.)
Remove unused sweeper code.
Rename blast_makeflow to makeflow_blast.
Rename bwa_makeflow to makeflow_bwa.
Add parrot as prefix to cms and atlas apps.
Rename to wq_replica_exchange.
Move wq_maker from biotools to apps directory.
Rename wq_maker.
Don't install any of the apps.
Move wq_sort to apps directory.
Fix Makefile to reflect new location of wq_sort.
Remove maker_galaxy as we now have the new wq_maker.
Minor edits to help string.
README for WQ replica exchange.
Remove .py extension from filename.
Updates to WQ sort from the TCC journal work.
README file for WQ sort.
Add sample input file for sorting.
Fix typo.
README file for WQ MAKER.