Update instruction to allow for running locally (not through docker)

[AlexAxthelm]

          Once we merge in this batch, I'll go through and see if I can get it working on bare metal? I think if mostly involves changing some things in the docker-compose, but dealing with variable inheritence across this and #71 open at the samer time is tricky.

Originally posted by @AlexAxthelm in #66 (comment)

[jdhoffa]

The main purpose of this workflow is to:

• Scrape index data
• Pull a transition monitor image and run PACTA on the scraped data

As such it is fundamentally dependent on building off of a base workflow.transition.monitor docker image:

workflow.prepare.pacta.indices/Dockerfile

Line 1 in c3502ea

FROM ghcr.io/rmi-pacta/workflow.transition.monitor:main

At this stage, I don't plan to support an API to run this through RStudio as it would either involve:

• jumping through hoops to figure out how to also run "Transition Monitor" itself through RStudio (e.g. by cloning the relevant repositories and calling source() on the scripts)
• adding some system() lines in the .R script to run the Docker image

Neither of these options seem to be worth the extra maintenance burden.

If either of you see it differently and wish to assign yourself this ticket then go ahead, otherwise I will close this issue.

FYI @cjyetman

[AlexAxthelm]

Closing as noted above.