BCBI-base: Julia packages commonly used by the Brown Center for Biomedical Informatics (BCBI)

Usage

cd /path/to/desired/location
git clone https://github.com/bcbi/BCBI-base
cd BCBI-base
julia --project install.jl

Creating custom environments

It is easy to create custom environments that contain any combination of packages.

mkdir my_environment_name
cd my_environmnent_name
touch Project.toml
julia —-project

Now that you are in Julia, you can add the specific combination of packages that you want. For example, the following commands will add DecisionTree, GLM, and PredictMD to your environment:

import Pkg
Pkg.add([“DecisionTree”, “GLM”, “PredictMD”,])

Troubleshooting

If you encounter an error, try running the following two lines:

julia --project clean.jl
julia --project install.jl

If this does not resolve the error, try running the following three lines:

rm -rf $HOME/.julia
julia --project clean.jl
julia --project install.jl

If you are still encountering an error, please open a new issue.