RefChef

RefChef is a reference management tool used to (1) document the exact steps undertaken in the retrieval of genomic references, (2) maintain the associated metadata, (3) provide a mechanism for automatically reproducing retrieval and creation of an exact copy of genomic references.

Installation

To install from PyPI using pip:

pip install refchef

To install using Anaconda Python:

conda install -c compbiocore refchef

Development

To install a development version from the current directory:

git clone https://github.com/compbiocore/refchef.git
cd refchef
pip install -e .

Run unit tests as: python setup.py test

Set up .env file with GitHub Access Token

Sensitive environment variables are stored in the .env file. This file is included in .gitignore intentionally, so that it is never committed. - Create a .env file and copy into it the contents of .env.template - Get your GitHub Access Token and add to the .env file.

Contributing

Contributions consistent with the style and quality of existing code are welcome. Be sure to follow the guidelines below.

Check the issues page of this repository for available work.

Committing

This project uses commitizen to ensure that commit messages remain well-formatted and consistent across different contributors.

Before committing for the first time, install commitizen and read Conventional Commits.

pip install commitizen

To start work on a new change, pull the latest develop and create a new topic branch (e.g. feature-resume-model, chore-test-update, bugfix-bad-bug).

git add .

To commit, run the following command (instead of git commit) and follow the directions:

cz commit

Contact

Contact [email protected] - this is our general help line, so please specify that your issue is with this site's contents