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docs(docker): add docker installation instructions (cytomining#409)
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d33bs authored Apr 26, 2024
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28 changes: 26 additions & 2 deletions README.md
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Expand Up @@ -22,20 +22,44 @@ For DeepProfiler, we include single cell processing tools in [pycytominer.cyto_u

From the single cell output, pycytominer performs five steps using a simple API (described below), before passing along data to [cytominer-eval](https://github.com/cytomining/cytominer-eval) for quality and perturbation strength evaluation.

The best way to communicate with us is through [GitHub Issues](https://github.com/cytomining/pycytominer/issues), where we are able to discuss and troubleshoot topics related to pycytominer.
Please see our [`CONTRIBUTING.md`](https://github.com/cytomining/pycytominer/blob/main/CONTRIBUTING.md) for details about communicating possible bugs, new features, or other information.

## Installation

You can install pycytominer via pip:
You can install pycytominer using the following platforms.
This project follows a `<major>.<minor>.<patch>` semantic versioning scheme which is used for every release with small variations per platform.

**pip** ([link](https://pypi.org/project/pycytominer/)):

```bash
# install pycyotminer from PyPI
pip install pycytominer
```

or conda:
**conda** ([link](https://anaconda.org/conda-forge/pycytominer)):

```bash
# install pycytominer from conda-forge
conda install -c conda-forge pycytominer
```

**Docker Hub** ([link](https://hub.docker.com/r/cytomining/pycytominer)):

Container images of pycytominer are made available through Docker Hub.
These images follow a tagging scheme that extends our release sematic versioning which may be found within our [`CONTRIBUTING.md` Docker Hub Image Releases](https://github.com/cytomining/pycytominer/blob/main/CONTRIBUTING.md#docker-hub-image-releases) documentation.

```bash
# pull the latest pycytominer image and run a module
docker run --platform=linux/amd64 cytomining/pycytominer:latest python -m pycytominer.<modules go here>

# pull a commit-based version of pycytominer (b1bb292) and run an interactive bash session within the container
docker run -it --platform=linux/amd64 cytomining/pycytominer:pycytominer-1.1.0.post16.dev0_b1bb292 bash

# pull a scheduled update of pycytominer, map the present working directory to /opt within the container, and run a python script.
docker run -v $PWD:/opt --platform=linux/amd64 cytomining/pycytominer:pycytominer-1.1.0.post16.dev0_b1bb292_240417 python /opt/script.py
```

## Frameworks

Pycytominer is primarily built on top of [pandas](https://pandas.pydata.org/docs/index.html), also using aspects of SQLAlchemy, sklearn, and pyarrow.
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13 changes: 13 additions & 0 deletions docs/install.rst
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Expand Up @@ -12,3 +12,16 @@ You can also install pycytominer with conda:
.. code-block:: bash
conda install -c conda-forge pycytominer
Docker Hub container images of pycytominer are made available through Docker Hub.
These images follow a tagging scheme that extends our release sematic versioning which may be found within our [CONTRIBUTING.md Docker Hub Image Releases](https://github.com/cytomining/pycytominer/blob/main/CONTRIBUTING.md#docker-hub-image-releases) documentation.

.. code-block:: bash
# pull the latest pycytominer image and run a module
docker run --platform=linux/amd64 cytomining/pycytominer:latest python -m pycytominer.<modules go here>
# pull a commit-based version of pycytominer (b1bb292) and run an interactive bash session within the container
docker run -it --platform=linux/amd64 cytomining/pycytominer:pycytominer-1.1.0.post16.dev0_b1bb292 bash
# pull a scheduled update of pycytominer, map the present working directory to /opt within the container, and run a python script.
docker run -v $PWD:/opt --platform=linux/amd64 cytomining/pycytominer:pycytominer-1.1.0.post16.dev0_b1bb292_240417 python /opt/script.py

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