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.

Small updates to many yaml files.  All peak callers now generating successfully.  Adjusted file_list input loding.  Fixed chip-job-ccat-format-bed to create correct number of columns.

This reverts commit 837c6fdd.

Updated format bed script.  Removed unnecessayr libraries, and removed reference to ladunga's home directory.

Renamed scripts with chip-prefix and hyphens.  Added new workflow generation script.  Removed yaml files from scripts dir.

This is the V3 of the Rscript for running csaw from the command line using YAML (see in a separate file). This  will be complemented with masking the blacklisted genomic regions from Anshul Kundaje for human and mouse.

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.