Added option to prevent saving files to database.  Updated generator handling of save_db & rewrite arguments.  Minor style fixes & comment updates.  Chip-gen now supports --save-db option.

Updated workflow parsing to require a properties file.  Executable loading is now done based on the provided chipathlon_bin path.

Fixed a lot of minor syntax errors.  Added missing xml closing tags.  Added validation for execute & output sites.

Added validation for making sure output / execute sites are defined in configuration.  Added new tester configuration files.

Added correct wrapper to avoid calling module load from python script.  Update run_music.py script to correctly format final result data.

Added rewrite option to pass to module_generators.  Updated module generators to allow module yaml to specify db saving & prefix type.

Gem ONLY accepts chr_fasta files with names chr1.fa, chr2.fa... We can't prefix them with our unique genome prefix, so we are now staging them into separate directories based on assembly.

Added warning for param file that exists but is empty.  Correctly add run parser errors to workflow.

Updated workflow validation steps to avoid throwing runtime exception unnecessarily.  Workflow now loads param file and passes correct params to each workflow job.

Removed unused _download_from_gridfs function in workflow.py.  Functino now exists in module_generator.

Adjusted remove_duplicates generator adn workflow to enable starting from bam files instead of fastq files.