BINF301-code

This code base is using the Julia Language and DrWatson to make a reproducible scientific project named

BINF301-code

To (locally) reproduce this project, do the following:

0. Download this code base. Notice that raw data are typically not included in the git-history and may need to be downloaded independently.
1. Open a Julia console and do:

   julia> using Pkg
   julia> Pkg.add("DrWatson") # install globally, for using `quickactivate`
   julia> Pkg.activate("path/to/this/project")
   julia> Pkg.instantiate()
   

This will install all necessary packages for you to be able to run the scripts and everything should work out of the box, including correctly finding local paths.

You may notice that most scripts start with the commands:

using DrWatson
@quickactivate "BINF301-code"

which auto-activate the project and enable local path handling from DrWatson.

Downloading datasets

To run the notebooks in the notebooks folder locally, you need to download and save several datasets in the right location. The datasets are stored on JuliaHub and can be downloaded by running the download_processed_data.jl script in the src folder. After downloading, the datasets will be saved in the data/processed folder.