Allow function to be called with inputs from Batch run script. Add co…

[cacerca]

Changes to from_specified_markers.py to allow for AWS Batch usage. The changes do the following:

• Allow for an input configuration to be passed in alongside a configuration path and command line inputs.
• Allow running the algorithm with no query for a pure "setup" run
• Add a flag to conditionally copy the files to a tmp directory as this is not needed in the Batch system.

[danielsf]

This functionality has been achieved by other changes, namely

a) introduction of argschema as a dependency b) implementation of the file_tracker.FileTracker class