Simple CompBio Project

A script for creating computational biology projects.

What does this script do?

1. Create a new project directory (name provided by the user).
2. Create files and subdirectories in that directory.
3. Initialize that directory as a Git repository.

Project Structure

The make-project.sh script creates a new project directory with the following structure:

example
├── CITATION.cff
├── README.md
├── bin
├── data
│   ├── anthro
│   ├── derived
│   └── raw
├── docs
├── notebooks
├── results
└── src

Usage

$ bash /path/to/compbio-project-script/make-project.sh <project-directory>

The script will create <project-directory>. If <project-directory> already exists, the script will exit with an error.

You can use a relative path to create a new project directory in the current working directory:

$ bash /path/to/compbio-project-script/make-project.sh example
$ cd example

Or you can use an absolute path to create a new project directory anywhere (as long as the parent directory already exists):

$ bash /path/to/compbio-project-script/make-project.sh /path/to/example
$ cd /path/to/example

Installation

1. Fork this repo by clicking the 'Fork' button above.

2. Clone the repo to your computer:

   $ git clone https://github.com/<your-GitHub-username>/compbio-project-script.git
   $ cd compbio-project-script
   

3. Edit the script to create the project directory structure of your liking.

4. Optional: Create an alias for this script so that you can run it easily from anywhere. To do so, you can add the following to your .bashrc (or .zshrc):

   alias mkprj='bash /path/to/compbio-project-script/make-project.sh'
   

   Restart your terminal/shell or source .bashrc to set up the alias.

   Then, you can run this script as:

   $ mkprj /path/to/your-make-project
   

Acknowledgements

• Forked from chendaniely/computational-project-cookie-cutter (Chen et al., 2015)

References

1. Chen, D., Gonzalez, I., & Loyall, D. (2015). computational-project-cookie-cutter: DOI Release (v.0.1.2). Zenodo. https://doi.org/10.5281/ZENODO.16558
2. Noble, W. S. (2009). A Quick Guide to Organizing Computational Biology Projects. In F. Lewitter (Ed.), PLoS Computational Biology (Vol. 5, Issue 7, p. e1000424). Public Library of Science (PLoS). https://doi.org/10.1371/journal.pcbi.1000424