Adding Benchmark scripts and outline for run-pipeline.py

[lyskov]

@gjoni @minkbaek this pull request is a follow up to our last meeting. It adds:

• outline for run-pipeline.py (ie Python rewrite of run_pipeline.sh script)
• add script to install dependencies (part of run-pipeline.py script now)
• add scripts needed for Benchmark integration

[lyskov]

@gjoni @minkbaek the most interesting part of this PR is run-pipeline.py script: https://github.com/RosettaCommons/trRosetta2/pull/6/files#diff-2be9fbbd387c71ba7ea9c2ce88ceffacfdd1e8bc5a46da66a72ce38e3d375437R1

I have moved install_dependencies into it since it looks like a good place for it. The actual run_pipeline function is now empty (https://github.com/RosettaCommons/trRosetta2/pull/6/files#diff-2be9fbbd387c71ba7ea9c2ce88ceffacfdd1e8bc5a46da66a72ce38e3d375437R82-R84) so this will need to ported. Please let me know how do you want to proceeds from here: we have choice of porting pipeline script or we can just call it. I prefer former since re-implementing in Python will give us more control on how to present results.

Thanks,

[lyskov]

👍