bb_project_setup - ampinzonv/BB3 GitHub Wiki

Function: bb_project_setup

Set up a standardized directory structure for a bioinformatics project.

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🔍 Description

This function creates a well-organized template of folders and documentation files for a new bioinformatics project. The structure follows community best practices and is inspired by resources like:

• Noble (2009), A Quick Guide to Organizing Computational Biology Projects: https://doi.org/10.1371/journal.pcbi.1000424
• Bioinformatics Core Training: https://bioinformatics-core-shared-training.github.io/shell-genomics/07-organization

“Someone unfamiliar with your project should be able to look at your computer files and understand in detail what you did and why.” — Noble, 2009.

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📁 Created Structure

20240605-ProjectName/
├── about.md
├── analysis/
│   ├── 01/
│   ├── 02/
│   ├── 03/
│   ├── 04/
│   └── README.analysis.md
├── data/
│   ├── raw_data/
│   ├── other_data/
│   └── README.data.md
├── docs/
│   └── README.docs.md
├── manuscript/
├── notebook.md
├── results/
│   └── README.results.md
├── sandbox/
│   └── README.sandbox.md
├── tmp/
│   └── README.tmp.md
├── tools/
│   ├── scripts/
│   ├── soft/
│   └── README.tools.md

Each directory includes a pre-filled README and/or placeholder content to help you document your process from the start.

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📥 Input

• The user must specify a project name via --project_name.
• No positional arguments are allowed.

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📤 Output

• A fully initialized project folder in the current directory.

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🧪 Examples

Create a project folder named "my_project":

bb_project_setup --project_name my_project

Force overwrite if the folder already exists:

bb_project_setup --project_name my_project --force

Run silently:

bb_project_setup --project_name test_project --quiet

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⚙️ Usage

bb_project_setup --project_name NAME [--quiet] [--force]

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🧵 Options

Option	Description
--project_name	Name of the project (required)
--quiet	Suppress informational messages
--force	Overwrite project directory if it already exists

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📌 Notes

• Automatically adds the current date (YYYYMMDD) as a prefix to the project directory name.
• Creates markdown-formatted README files to help organize and document project activities.
• Protects raw_data by recommending chmod -R -w after setup.