Merge branch 'develop' into topic_CuffdiffCall
Merge branch 'develop' into topic_CuffdiffCall
clean up
More clean up
Merge branch 'develop' into topic_CuffdiffCall
topic_CuffdiffCall:
src/blacktie/utils/calls.py:
first pass class def
       modified:   docs/_build/doctrees/code.doctree
       modified:   docs/_build/doctrees/environment.pickle
       modified:   docs/_build/doctrees/project.doctree
       modified:   docs/_build/doctrees/tutorial.doctree
       modified:   docs/_build/html/code.html
       modified:   docs/_build/html/genindex.html
       modified:   docs/_build/html/objects.inv
       modified:   docs/_build/html/searchindex.js
topic_print_cmds:
src/blacktie/scripts/blacktie_pipeline.py
src/blacktie/utils/calls.py
topic_print_cmds: 
- changed focus to BaseCall methods to print cmds and check for --dry-run status
- silenced logs and ensured a net file/folder increase of ZERO

FILES:
src/blacktie/scripts/blacktie_pipeline.py
src/blacktie/utils/calls.py
Merge branch 'topic_print_cmds' into develop
src/blacktie/scripts/blacktie_pipeline.py:
- typo correction in help text
Merge branch 'develop' into topic_CuffdiffCall
topic_CuffdiffCall: fixed get_mask_file and added cuffdiff loop in the script
topic_CuffdiffCall:
Merge branch 'topic_CuffdiffCall' into develop
src/blacktie/utils/calls.py:
- fixed problem in CuffdiffCall.get_cuffmerge_gtf() that came from adptign it from CufflinksCall.get_bam_path()
src/blacktie/utils/calls.py:
- added missing ``if not self.dry_run:`` statements in a few Call class methods that I had overlooked
topic_sge_scripts:
- Added preliminary ability to generate qsub scripts instead of running the analysis itself
Merge branch 'topic_sge_scripts' into develop
Merge branch 'develop'