terra-jupyter-base should preserve /home/jupyter contents and environment variables such as PATH

[droazen]

Currently, in images derived from terra-jupyter-base, it appears that the /home/jupyter directory is completely blown away after docker build and overwritten with a Terra persistent disk mount. Likewise, environment variables such as PATH set during docker build are not preserved. At least, this has been my experience while testing https://github.com/broadinstitute/gatk-workshop-terra-jupyter-image/blob/main/Dockerfile

The consequence of this is that there's no way to properly set up the jupyter user's environment and configuration during docker build. I had to resort to asking users of our image to run a script live in a terminal in their Terra workspace before loading their notebooks, in order to restore some necessary configuration to /home/jupyter

[dvitale199]

I'm running into this same issue. How did you go about setting the missing env variables?