Tried changes to accomodate ihg production.  This commit isn\'t working.
Fixed issues with finishing casava (merging and initiating following pipelines).
Add the ability to read --__ dictionary from description.  Also fixed bug in submitting pipeline.  Added spliton , to steps so that each step and not each character is a key.
Added emails to dnanexus model.
Separated the prepending string to file from the __link_to_web_portal__ method to its own function.  Also added a bunch of debugging messages and the tracking of sample sheet within the Seq Run object (allowing external specification of this file).  Finally, added a method to handle pipelines that are conducted on flowcells instead of samples (like the DNA_nexus pipeline) that are launched after casava.  Wish list:  Need to consolidate the launching of pipelines here and in processes/control.py function that pushes directories into pipelines according to input arguments --- also should separate out that functionality.
Forgot the necessary __init__.py in the my_utils directory.
Separated out the addition of sequencing run objects from the maintanence function so that this functionality can be called directly from data_management_pipeline or another script if desired.
Added option to specifiy if meta data should be printed when sample sheet is printed.  This allows us to specify False so that only the sample sheet is printed.  Also, added code to handle a bug that was not identifying 0 in the index length when an index like AGCTGCTA is used on the same flowcells as a double index like AGCTGCTA-CGGACAAT.
Fixed issue so that the parsed sample sheet now has the SampleID in it from the initial sample row.
Fixed next step calling in pipelines so that no sample is necessary (for steps that are doing other objects like flowcells).  Also added code to handle the first step i the pipeline (need to consolidate code elsewhere for this generalization).  Replaced pipeline with Pipeline, as it should be (bug-fix) and added pipeline_key to the initialization of the pipeline when pipeline_key is available.  Finally, added a function that intializes flowcell pipelines from a source dir although this function should be consolidated with the automated version of this.
Trying to handle a bug that is unable to launch Summary Stats because a directory is already cleaned.  I think this was a result of multiple of the same pipelines being initialized on the same day.  If the expected files are now missing from the output of Bcbio, return False.  May need to change this back once the larger issue is addressed.
Check to make sure the snp dir is present before assigning the snp_path.  Also, fixed bug where is comple was missing additional arguments.
Now checking the root directory in list sample dirs for Sample_ since Undetermined_indices also contains a SampleSheet.csv file.
Apparently, casava needs no n's when the length of the index is 0.
set the print_meta_data variable to false so that the merge option is actually functional (Diya requested this functionality, and it was simple enough to do.)
Defaults is complete to the SampleQsubProcess.__is_complete__ already.  Also, am trying to handle a bug where the vcf file is lost.  Have added functionality to search for it.  Need to see if it works.
Is complete already addressed by inheritence.
Added the ability to (re)add a sequencing run to database for management.  Also, added the ability to launch a flowcell pipeline from the command line.
If the first step of a running pipeline has not begun, begin it.  Also, corrected the complete file check logic.  Also, adjusted the hiseq run number so that it will appear in my code as 4 digits.  Next, I am now keeping track of the SampleSheet.csv file in the BclToFastqPipeline (so that it may be adjusted at the command line).  Finally, I debugged the DNANexusPipeline so that it works.
Added NGv2 pipeline and the configuration for the flowcell pipeline to be used in the flowcell (non-sample) pipeline functions.  Added DNANexus library to classes so that the models.py file could be detected.