update docker scripts to not clone from github or use static copies of the source

[hjwilli]

Part of the docker setup process for all three containers clones pennai:master into /opt/. The docker build process seems to rely on /opt/ (for example the lab Dockerfile runs 'RUN npm install...' from /opt/). The running containers seem to optionally rely on the contents of /opt/ or the local version of pennai as exposed via a docker shared drive.

This seems confusing and error prone, especially if there is a mismatch between local files and github master. Determine if there was a reason for cloning the project (perhaps as part of AWS deployment?). If it makes sense, update the deployment scripts to copy from the local to /opt/ instead of cloning from github. Attempt to copy only what is necessary for the given container (see #34)

• Move git clone from the base docker image to lab, machine, dbmongo
• Remove git clone from lab
• Remove git clone from machine
• Remove git clone from dbmongo

[weixuanfu]

OK, I will work on this line

[hjwilli]

After discussion with @weixuanfu, there doesn't seem to be a good reason to clone from github, this will be removed.

[weixuanfu]

I just pushed some commits to pennai_lite branch to remove git clone in those containers.

[hjwilli]

Clone has been removed, a static compressed file of a portion of the codebase is now being used to populate /opt. It seems like this is being used to configure how anaconda is set up, may also be used for data initialization for machine, lab and dbmongo.

Will try to factor out the need to copy some of the source tree into /opt.