10  OpenSAFELY repositories

• OpenSAFELY is a system of Python packages (opensafely and cohortextractor) which run various Docker containers
  • The main GitHub organisation page is here
  • All the core code is published in their opensafely-core organisation on GitHub here
  • And there is also their opensafely-actions organisation here
• A Docker container is a like a virtual machine
  • It defines the operating system and programs running within it
  • On my Windows 10 machine I can run an Ubuntu docker container
  • Just because an R package is installed in the R installation on your machine does not mean that it is installed in the OpenSAFELY R Docker container
    • See the list of packages in the R Docker container here

10.1 Demo repo

• Have a look at the demo repo here

10.2 Getting started

• See OS page here

• If creating a new repo create from the OS template here

  

• This is already Git initialized

• Important files

  • project.yaml
    • Defines the jobs and the order in which they run
  • /analysis/study_defintion.py
    • Defines the study population extracted from the OpenSAFELY database
    • This should return .csv file/s of data to read into R
  • /analysis/##_R-scripts.R
    • Your analysis scripts

10.3 Running jobs (on the dummy data)

There are a couple of ways to run jobs on the dummy data system.

• In your OpenSAFELY repo online
  • Use Gitpod
• On your own machine, in which case please install the following free software
  • If on Windows - Windows Subsystem for Linux version 2, using the instructions here
  • Docker Desktop, from here
  • Python (described on a previous page here)
  • Git (described on previous page here)
  • GitHub Desktop, from here
  • VSCode text editor, from here