fhcrc/deenurp — pull request #7 by nhoffman (2013-12-31 01:16:20+00:00)
Title: 04 infernal1.1

Untested with MPI - we may still want to remove MPI support rather than worry about it. Also, cmalign 1.1 uses all available cores unless a smaller number is specified. We may want to limit that either optionally or by default.