10 OpenSAFELY repositories
- OpenSAFELY is a system of Python packages (opensafely and cohortextractor) which run various Docker containers
- 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