Environment

conda (python and base R)

Base R, python, and all python packages are installed via the conda utility. To set up the conda environment, run the following from the root directory

conda env create -f environment.yml

and follow instructions output in terminal.

R packages

The base R installation is done through conda but most R packages are installed through R. The file r_packages.csv contains all installed packages & versions. These should be installable via install_version() from the devtools package.

Project pathing

Developer configuration file

Make sure you have a file, dev_paths.txt, in the root project directory laid out as follows (do not include comments):

root/path/for/storing/data      # location of data to be analyzed
root/path/for/storing/analysis  # location of analysis output (usually .csv files)
root/path/for/storing/figures   # location of figure and visualization output
<blank line>

Directory verification script

Run

python verify_dirs.py

from the project root. This will verify that all needed files/directories exist. This script will also create all needed output directories for analysis and figures.

Custom utilities

This project has custom packages (rutils and pythonutils) that must be installed in the conda environment. Installations will only occur within the conda environment and should not affect any other R or python installations on your system.

rutils

Change to the rutils directory and run

Rscript setup.R

All custom R utilities should now be installed in the conda environment.

pythonutils

Change to the pythonutils directory and run

python setup.py

All custom python utilities should now be installed in the conda environment.