Add override mechanism for Cytoscape container

[agitter]

#464 adds the ability to override containers for all of the pathway reconstruction algorithms. Tristan noticed that this implementation does not support overriding Cytoscape. He left one possible implementation strategy if we need to support Cytoscape overrides: #464 (comment)

[agitter]

LPCA in #500 is another Docker image that runs outside of the pathway reconstruction run step.