Added insertsize metrics.
Added bowtie helper.
Added qsub pipeline runner for bowtie.
Added bowtie pipeline script.
Updated jobs to run.
Fixed bug with bowtie output.
Updated.
Changed way of running Popen.
Updated.
removed job_stderr from job runners.
Added tophat wrapper.
Added tophat pipeline helpers.
Added tophat wrapper.
Removed some debugging from Tophat wrapper init.
Added exome pipeline script
Added tasks
Updated utils
Updated mutect params.
Updated other stuff
Added method to change bfast executable.