Merge branch 'hotfix/cython' into develop

Conflicts:
	nextgen/bcbio/solexa/samplesheet.py
Merge branch 'hotfix/cython' into develop
Merge conflict
Merge branch 'develop' of https://github.com/SciLifeLab/bcbb into develop
Merge branch 'hotfix/picard-tools' into develop
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' into develop
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
Added patch to work with both default Ubuntu/Debian picard-tools package and with jars directory. Thanks @chapmanb