Since fabric is a dependency in setup.py, removed the try statement in transfer.py
Formatting
Refactored a try block to a dict.get() call
Added a funciton for simple rsync uploading in illumina_finished_msg.py
Merge branch 'hotfix/libsam-java'
Merge pull request #235 from guillermo-carrasco/master

Picard issues with the pipeline
Refactored _post_process_run in illumina_finished_msg.py, now has a push_data flag.
Also, all flags are now optional with defaults of False.
Reformatted the kwargs in the call for main in illumina_finished_msg.py for increased readability
Test that _post_process_run is called in the right way from initial_processing
Testing that _post_process_run can be called as in process_first_read
Defined analyze function in toplevel.py
Defined 'analyze' task which doeas what 'analyze_and_upload' does but without fetching files
Made illumina_finished_msg send 'analyze' message if data have been pushed and should be processed
Added CLI flag for pushing data in illumina_finished_msg.py
Some formatting
Merge pull request #236 from guillermo-carrasco/develop

Support for default picard-tools
Fixed rsync command in simple_upload within illumina_finished_msg
to correspond to how subprocess.check_call works.
Added flag for not starting casava conversion/demultiplexing
Various fixes that finally will send relevant information over celery when pushing
Included some preliminary support for starting analysis on pushed data