Add timing information to the RNA-seq pipeline.
Added information for fixing conda.cli not found issue.

Thanks to Jiantao Shi.
Fix for Cufflinks dropping high-coverage genes.

Set --max-bundle-frags to 2000000, up from the default of
1000000. Thanks to @mjafin for the suggestion and
discussion.  Closes #357.
Update of changes in preparation for the 0.7.8 release.