Added valid_sample checking in database.  Fixed db_save_results to use sample ids.  Adjusted memory request usage for spp & db_save.

Create save_result function in workflow.  Updated workflow_job & module to provide additional necessary info to save database results.

Added db_save_results yaml job, and script.  Updated workflow information tracking to create correct meta data files for saving information to the database.  Conf adjusted to support yaml files, and arbitrary result files.  workflow_job can now return a dictionary of all arguments used.

Added bed & peak file saving functionality to the database class.  Updated testing script to use unittests.  Updated experiment_from_samples script to only print out unique values.  Added list of current tools to conf.

Updated peak_call yaml & jobs.  Fixed r_spp wrapper to handle bad argparsing.  Updated conf to include list of system commands.

Fixed param files to reference correct commands.  Updated workflow job loading to use commands specified within yaml files.  Added a debug mode to workflow to print out additional statements.

Updated conf to include tagalign files.  Renamed script files from wrappers.  Added cat_spp for ungzipped results.  Updated peak_call.yaml to rename .bed files to .tagAlign for spp.

Fixed issues with submitting multiple jobs for same files.  Added new example to find experiment_ids from the T4 and HM collections. Download now prioritizes hcc_url if it exists.

Make sure the `conn` variable exists, otherwise a `urllib2.URLError`
exception causes a subsequent `UnboundLocalError` in the `finally`
block.

Updated stdout & stderr redirection.  Includes adjustments in individual job yaml files, module yaml files, and workflow generation handling.

Fixed reference to undefined variable key in workflow_module.  Adjusted param files to use bed arguments

Fixed typo in remove_duplicates.yaml.  Adjusted get_full_name to handle no markers.  Updated workflow to track prefixes cross module.