|
| 1 | +# BiocPy Environments |
| 2 | + |
| 3 | +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. |
| 4 | + |
| 5 | +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). |
| 6 | + |
| 7 | +--- |
| 8 | + |
| 9 | +## Getting Started |
| 10 | + |
| 11 | +### Using Conda or Mamba |
| 12 | + |
| 13 | +To create an environment using one of the configuration YAML files: |
| 14 | + |
| 15 | +```shell |
| 16 | +# Use conda or mamba to create the environment |
| 17 | +conda env create -f envs/release.yml |
| 18 | + |
| 19 | +# Activate the environment |
| 20 | +conda activate biocpy_release |
| 21 | + |
| 22 | +# Check the versions of the installed packages |
| 23 | +pip list |
| 24 | +``` |
| 25 | + |
| 26 | +> **Note**: If you have multiple Conda channels enabled, you may need to set the channel priority for reliable package resolution: |
| 27 | +> |
| 28 | +> ```sh |
| 29 | +> conda config --set channel_priority flexible |
| 30 | +> ``` |
| 31 | +
|
| 32 | +--- |
| 33 | +
|
| 34 | +### Using Docker |
| 35 | +
|
| 36 | +To create and use a Docker image based on the provided Dockerfile: |
| 37 | +
|
| 38 | +```sh |
| 39 | +# Build the Docker image |
| 40 | +docker build -f release.dockerfile -t biocpy_release |
| 41 | +
|
| 42 | +# Run the Docker container |
| 43 | +docker run -it biocpy_release |
| 44 | +``` |
| 45 | +
|
| 46 | +--- |
| 47 | + |
| 48 | +## Available Configurations |
| 49 | + |
| 50 | +### Conda Configurations |
| 51 | + |
| 52 | +- `envs/release.yml`: Contains the stable release versions of BiocPy and related packages. |
| 53 | + |
| 54 | +### Docker Images |
| 55 | + |
| 56 | +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: |
| 57 | + |
| 58 | +- `biocpy/release`: Based on `release.yml` |
| 59 | + |
| 60 | +You can pull these images directly: |
| 61 | + |
| 62 | +```sh |
| 63 | +## Replace the VERSION tag with an available version from the registry |
| 64 | + |
| 65 | +# Pull the stable release image |
| 66 | +docker pull ghcr.io/biocpy/environments/release:<VERSION> |
| 67 | +``` |
| 68 | + |
| 69 | +> **Note**: We might expand this to include both dev and release configurations of the packages. In that case: |
| 70 | +> `envs/dev.yml`: Includes the latest development versions of BiocPy packages for testing and contributions |
| 71 | +> `biocpy/dev`: Docker image based on `dev.yml` |
| 72 | +
|
| 73 | +--- |
| 74 | + |
| 75 | +## Support |
| 76 | + |
| 77 | +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). |
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