bfx_201903

To run this project for yourself, clone the repo from github.

Required:

• Command line tools:
  • tree
• conda env bfx_201903 (containing all python / R dependencies)
  • This can be cloned in entirety using ./conda_requirements.txt (if on linux)
    • conda create --name bfx_201903 --file conda_requirements.txt
  • Or constructed approximately (on unix-a-like)
    • conda env create --name bfx_201903 --file conda_environment.yaml
  • To activate:
    • conda activate bfx_201903

Warning:

• stackr will be installed from github during the run of code_tools.Rmd

Run:

• Open this R project in rstudio
  • rstudio bfx_201903.RProj &
• Open the code_tools.Rmd file within rstudio
• knit the document to generate the html presentation
• THIS WILL FAIL the first time you run it
  • it should fail when rosa_testable is imported
  • I think this is because the python/reticulate interpreter is started before the package is installed by bash/pip
• It should knit properly the second time you run it

Sphinx:

• The code in the section on Sphinx documentation is not run during compilation of the presentation
• To run this, just open the repo in the command line, under the bfx_201903 environment, and run the mentioned commands; eg
  • (cd rosa_cli && make docs)

Note:

• the code is actually incorrect....
  • it works ok for a permutation of the first N natural numbers (the requirements for the rosalind challenge)
  • but it fails on some sequences that contain duplicated elements
  • and, although it doesn't aim to deal with non-positive numbers, it doesn't throw an exception for this unexpected input