+ """
+ Build and run the bwa binary.
+
+ command is the bwa module, e.g., "index" or "aln".
+
+ command_args is a list of additional command line arguments, e.g.,
+ ['-a', 'bwtsw', 'ref.fasta']
+
+ It is assumed that we are running in a Crunch job environment, and
+ the job's "bwa_tbz" parameter is a collection containing the bwa
+ source tree in a .tbz file.
+ """