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Genome reference manager.

Project description


Travis Coverage Docs License PyPi

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.


To install from PyPI using pip:
pip install refchef
To install using Anaconda Python:
conda install -c compbiocore refchef


To install a development version from the current directory:

git clone
cd refchef
pip install -e .

Run unit tests as: python 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.


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.


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 - this is our general help line, so please specify that your issue is with this site’s contents

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