Merge pull request #51 from broadinstitute/dp-indels

fix some reworked assembly pipelines, improve some reports
Merge pull request #52 from broadinstitute/dp-indels

reorganize, document, tune defaults
Merge pull request #53 from broadinstitute/dp-indels

re-parallelize, tune pipes, cleanups
Adjust verifycmd for MUSCLE

Without any command-line arguments, the behavior and exit code of the MUSCLE executable
depend on whether isatty(stdin). If that's not the case (as in certain unattended
environments, but evidently not Travis), it'll try to read from stdin and fail. Very
nasty to debug because it then works as expected when you try it interactively! Running
with -version is more predictable.
Merge pull request #54 from dnanexus/fix-muscle-tool-installer

Adjust verifycmd for MUSCLE
Merge remote-tracking branch 'origin/master' into dp-indels