[biocterm] [biocswirl] Implement contained installations

[lisancao]

[biocterm] [biocswirl] Implement contained installations

About: Installations are currently pretty messy, particularly with R as going through a course will install a LOT of packages, and it's unclear whether swirl has a clean uninstall feature. As we work on multilanguage workflows it becomes more and more important for us to have contained environments for courses, especially if our installs overwrite packages someone already has. Should also prompt user if they want to use their install or keep it contained.

Tasks

• Explore options of either using Docker or Singularity Containers (multilanguage workflows) or working with beRi (Bioconductor workflows)
• Prepare singularity recipes for respective courses (will also have to use Rocker) and execute from BiocTerm

Resources

https://singularity.lbl.gov/

(Workflow managers)
Nextflow
https://www.commonwl.org/v1.0/CommandLineTool.html

Tag can be

biocswirl(related to course material)
biocterm (interface changes)
dev      (developers only)
file     (changes to file and folder structuring) 
rpkg     (r package/usethis and CRAN documentation changes)
feat     (new feature)
fix      (bug fix)
refactor (refactoring code)
style    (formatting, missing semi colons, etc; no code change)
doc      (changes to documentation)
test     (adding or refactoring tests; no production code change)
version  (version bump/new release; no production code change)
dbg      (Changes in debugging code/frameworks; no production code change)
license  (Edits regarding licensing; no production code change)
hack     (Temporary fix to make things move forward; please avoid it)
WIP      (Work In Progress; for intermediate commits to keep patches reasonably sized)