BiocPy Environments

This repository provides Conda/Mamba configuration files and Dockerfiles to simplify the creation of environments containing most Python packages in the BiocPy (& friends) ecosystem. These provide easy setup for users looking to use the BiocPy tools.

In addition, pre-built Docker images for these configurations are published to the GitHub Package Registry.

Getting Started

Using Conda or Mamba

To create an environment using one of the configuration YAML files:

# Use conda or mamba to create the environment
conda env create -f envs/release.yml

# Activate the environment
conda activate biocpy_release

# Check the versions of the installed packages
pip list

Note: If you have multiple Conda channels enabled, you may need to set the channel priority for reliable package resolution:
conda config --set channel_priority flexible

Using Docker

To create and use a Docker image based on the provided Dockerfile:

# Build the Docker image
docker build -f release.dockerfile -t biocpy_release

# Run the Docker container
docker run -it biocpy_release

Available Configurations

Conda Configurations

envs/release.yml: Contains the stable release versions of BiocPy and related packages.

Docker Images

Pre-built Docker images are available in the GitHub Package Registry. These images correspond to the provided Conda configurations:

biocpy/release: Based on release.yml

You can pull these images directly:

## Replace the VERSION tag with an available version from the registry

# Pull the stable release image
docker pull ghcr.io/biocpy/environments/release:<VERSION>

Note: We might expand this to include both dev and release configurations of the packages. In that case: envs/dev.yml: Includes the latest development versions of BiocPy packages for testing and contributions biocpy/dev: Docker image based on dev.yml

Support

If you encounter issues or have questions, please open an issue in this repository or reach out via the BiocPy GitHub Discussions.

BiocPy/environments

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