https://github.com/outlierbio/ob-project-template
Outlier Bio analysis project template
https://github.com/outlierbio/ob-project-template
Last synced: 5 months ago
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Outlier Bio analysis project template
- Host: GitHub
- URL: https://github.com/outlierbio/ob-project-template
- Owner: outlierbio
- Created: 2016-04-05T17:12:22.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2018-01-29T15:13:39.000Z (about 7 years ago)
- Last Synced: 2024-08-09T02:17:44.190Z (8 months ago)
- Language: Jupyter Notebook
- Size: 17.6 KB
- Stars: 54
- Watchers: 4
- Forks: 15
- Open Issues: 0
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Metadata Files:
- Readme: README.md
Awesome Lists containing this project
- jimsghstars - outlierbio/ob-project-template - Outlier Bio analysis project template (Jupyter Notebook)
README
# Outlier Bio project template
This is a [cookiecutter](https://cookiecutter.readthedocs.io/en/latest/index.html) template for data science projects. It sets up stubs for:
- **standard folder system** with `README.md` descriptions within each folder
- **Luigi build pipeline**, `build.py`, for downloads and batch preprocessing
- **Dockerized notebook server** for either Jupyter, RStudio, or RStudio with [Bioconductor](http://www.bioconductor.org/) packages pre-installed.
- **computational notebook** to run your analysis, either `notebook.ipynb` (if you use Jupyter) or `notebook.Rmd` (if you prefer RMarkdown).
Docker allows you to completely specify your enviroment so your analysis is fully reproducible. Just make sure to add all dependencies (e.g., apt-get for system packages, conda for Python, CRAN or Bioconductor for R) to the Dockerfile and, if applicable, the `install_packages.r` script used by the Dockerfile.
You can choose the server platform during initiation of the `cookiecutter` script, which will then adjust the Dockerfile accordingly.
## Get started
From a terminal, change to the directory you want to hold the project folder, and run cookiecutter:
`$ cookiecutter /path/to/ob-project-template`
Fill in the prompts (your name and email, project name and description, and the flavor of notebook platform) and it will be created for you! Be sure to double-check the auto-generated project slug and fix it if necessary–this will be the name of the folder.