computational-project-cookie-cutter

A cookie cutter (aka project template) to set up a folder structure for a computational project. This is a quick way to setup a folder structure that follows one standard to organize a project. This helps with project management, reproducibility, sharing, and publishing your data, analysis, and results.

This project was inspired (and modeled off) by:

Noble WS 2009 A Quick Guide to Organizing Computational Biology Projects. PLoS Comput Biol 5 7: e1000424. doi:10.1371/journal.pcbi.1000424

What it does

the setup_project_dir.sh script creates the following folder structure:

Path_Provided
|- doc/           # directory for documentation, one subdirectory for manuscript
|
|- data/          # data for storing fixed data sets
|
|- src/           # any source code
|
|- bin/           # any compiled binaries or scripts
|
|- results/       # output for tracking computational experiments performed on data

A README containing a brief blurb is placed in each folder. This is because git will not track empty folders and placing a README will remind you of what goes in each folder, and also the overall folder structure will be retained

How to install

There are a few ways set everything up.

1. fork/clone the repo to your computer
2. download and extract the zip on the right
3. download the script by clicking on setup_project_dir.sh above and right-click > save link as... on the raw button
4. downloading the script directly: wget https://github.com/chendaniely/computational-project-cookie-cutter/raw/master/setup_project_dir.sh

The above methods all accomplish the same thing, it gets the script onto your computer. Use which ever one makes sense.

How to use

go to the directory where the setup_project_dir.sh is and run the following line in your terminal

bash setup_project_dir.sh /directory/to/where/your/project/is

Enjoy!

Use it anywhere

If you want to be able to call this script no matter where you are, you can add the following lines to your .bashrc, .bash_alias, etc (Note: you only need it in one of them)

alias pinit='/path/to/where/the/script/is/setup_project_dir.sh'

and you can use it as such: pinit /path/to/folder or if you are already in the folder pinit .

Similar Projects

I'm not the only one creating similar cookie-cutter projects:

• https://github.com/Reproducible-Science-Curriculum/rr-init