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.

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.

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

Fixed minor issues in param yaml scripts. Updated workflow to add jobs and create relevant pegasus information.  Workflow can now generate download and alignment jobs, still needs testing.  Setup updated to include job-scripts.

Added genome validation.  Added module loading with minor validation.  Added required file detection in modules.

Added download script.  Updated job yaml.  Updated module yaml.  Add executable loading to workflow code.  Updated database validation for new inputs.

Added initial yamlJob class.  Added tester file for individual tests.  Added missing command entry to bwa_align_paired.yaml.  Added internal configuration