https://github.com/biocpy/environments
Conda configurations for managing BiocPy releases
https://github.com/biocpy/environments
Last synced: 4 months ago
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Conda configurations for managing BiocPy releases
- Host: GitHub
- URL: https://github.com/biocpy/environments
- Owner: BiocPy
- Created: 2025-01-24T16:25:51.000Z (about 1 year ago)
- Default Branch: master
- Last Pushed: 2025-01-24T21:40:04.000Z (about 1 year ago)
- Last Synced: 2025-05-22T02:07:39.400Z (9 months ago)
- Language: Dockerfile
- Size: 2.93 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# 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](https://github.com/orgs/BiocPy/packages?repo_name=environments).
---
## Getting Started
### Using Conda or Mamba
To create an environment using one of the configuration YAML files:
```shell
# 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:
>
> ```sh
> conda config --set channel_priority flexible
> ```
---
### Using Docker
To create and use a Docker image based on the provided Dockerfile:
```sh
# 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](https://github.com/orgs/BiocPy/packages?repo_name=environments). These images correspond to the provided Conda configurations:
- `biocpy/release`: Based on `release.yml`
You can pull these images directly:
```sh
## Replace the VERSION tag with an available version from the registry
# Pull the stable release image
docker pull ghcr.io/biocpy/environments/release:
```
> **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](https://github.com/biocpy/biocpy/discussions).