make FilterSamReads work in scenarios that create empty output files. start converting some samtools calls to pysam.
separate out tool installation tests before normal tests in Travis
revert samtools Tool wrapper to subprocess.call instead of pysam until we can fix Travis+pysam+nose
bugfix prinseq and make rmdup mvicuna work on bams with empty read groups
some more trinity thoughts, commented out for now [ci skip]
set get path for prinseq
add some logging [ci skip]
tune pipeline parameters and start consolidating some of the depletion pipe
consolidate hs_deplete steps [ci skip]
update reports and stats to be per seq run [ci skip]
argparse fixes for deplete_human
fix var
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
Merge pull request #55 from broadinstitute/dp-indels

updates to pipeline structure