create_project

This repo and README provides the code and information for how to create your standardised repository.

How

Use any of the different implamentation of the create_project function to create your project directory and initialise it.

you must provide 2 arguments:

• location: where you want to make the project.
• project: the name of the project.

Example:

1- You have downloaded (or cloned) this project with all its folders and subfolder on your local machine.

2- You would like to initilise a project on Osiris in your "Documents" folder and your username is doej, so you the path to your project will be /home/doej/Documents/.

3- The name of your project is foo_project.

4- Based on your preference, choose one of the following implementations to create your project directory.

R

you can use create_project() directly in R on Osiris

source("/data/IARC_Biostat/work/create_project/create_project.R")
create_project(
  location = "/home/doej/Documents/",
  project = "foo_project")

Or if you are not running on OSIRS but your personal computer.

source("/path/to/create_project/create_project.R")
create_project(
  location = "/home/doej/Documents/",
  project = "foo_project"),
  create_project_path = "/path/to/create_project"

bash

On a terminal, navigate to where this project is located (either a local copy or the copy on OSIRS: /data/IARC_Biostat/work/create_project/). Run create_project.sh with the following options:

cd /data/IARC_Biostat/work/create_project/
bash create_project.sh --location "/home/doej/Documents/" --project_name "foo_project"

python

you can use create_project() directly in python or a notebook on Osiris

sys.path.append('/data/IARCBiostat/create_project/create_project')
from create_project import create_project
create_project(
  location = "/home/doej/Documents/",
  project = "foo_project")  

General guidelines:

• use capitals sparingly
• use - to combine; e.g., colon-caner
• use _ to separate; e.g., EPIC_colon-cancer