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

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

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.

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!

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 .

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

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