If necessary: git clone git@github.com:Victoria-GS/rhds.git
Open the mamba environment: mamba activate rhds
To run a script: source scripts/config.r Rscript ${datadir} ${resultsdir}
This will copy the configuration template and enable your script to access the local project directories defined in our config.env file: cp config-template.env config.env
In the file type: datadir="/data//rhds/data" resultsdir="/data//rhds/results" docsdir="/data//rhds/results/docs"
Dont forget! Add config.env to .gitignore and add/commit/push to git so that git ignores the local paths: code .gitignore
We split run-analysis.r into: 1 extract-data 2 clean-clinical 3 predict-proteins 4 combine 5 analysis