chapter 4.1 - docker isn't the Hutch default config

[jayoung]

in this section: https://hutchdatascience.org/FH_WDL101_Cromwell/fred-hutch-customizations.html#standard-runtime-variables

the top bit says "These runtime variables are both the defaults for our Fred Hutch configuration" and it lists below docker: "ubuntu:latest".

Sounds from that like I will be working in a container by default, but I think I can tell (from some tests I just ran) that the default is NOT to run within a docker container. My test is this: I add which codeml to diy-cromwell-server/testWorkflows/helloHostname.wdl and I run it (codeml is something I installed in my own gizmo environment). When the runtime block is empty, which codeml succeeds in finding my executable (/home/jayoung/malik_lab_shared/linux_gizmo/bin/codeml), so I think it can't be running within a container. But if I add which codeml to helloSingularityHostname.wdl, where the docker container is specifically requested using docker: "ubuntu:latest", it returns nothing, as I would expect when running in the container.

Solution could be just to rewrite the top bit. Maybe a separate spot would be a good place to summarize the default Hutch config - simply discuss here common config options the user MIGHT want to mess with. Or just show after each of these options what the default actually is.

Also in the Hutch-specific section: is dockerSL: "ubuntu:latest" actually the default, as implied by that section's header? Again, maybe split out list of possible config variables from the list of defaults.

I also totally don't understand the thing about the soft links right now. It might get clearer once I actually start running stuff within containers/scratch. Examples might be the best way to help me see how I'd use that.

[vortexing]

ah yes, very good point. I'll re-think how I can reframe this regarding defaults on all this stuff. the docker, dockerSL and modules all need more clear info about that.