This repo contains an environment definition and automated build for the "ndutils" Python environment used for analysis of N-dimensional microscopy data. The environment is maintained by the Computational Microscopy platform at the Chan Zuckerberg Biohub - San Francisco and is available on the bruno high performance compute cluster.
If you have access to bruno you can load this shared environment using
module load anaconda comp_micro
conda activate ndutilsThis environment is versioned, and a list of previous versions is available under Releases.
You can check the version of the installed environment using the env_version command, using with "pip list", or with "pip show".
$ env_version
ndutils 0.2.0.dev3
$ pip list | grep ndutils
ndutils 0.2.0.dev3
$ pip show ndutils
Name: ndutils
Version: 0.2.0.dev3
Summary: ndutils compute environment for computational microscopy at CZBiohub SF
...
You can install your own copy of this environment in the following ways. See the available releases at https://github.com/czbiohub-sf/compmicro-ndutils-env/releases.
python3 -m pip install git+https://github.com/czbiohub-sf/compmicro-ndutils-env.git@v${RELEASE_VERSION}
git clone [email protected]:czbiohub-sf/compmicro-ndutils-env.git
cd compmicro-ndutils-env
git checkout v${RELEASE_VERSION}
conda env create --file=environment.yml
A docker image is automatically built using GitHub actions whenever a version tag is pushed. See the GitHub-hosted compmicro-ndutils-env Docker repository.
To pull and run a Docker image:
docker run ghcr.io/czbiohub-sf/compmicro-ndutils-env:v${RELEASE_VERSION}
To run an Apptainer container created from the Docker image:
apptainer run docker://ghcr.io/czbiohub-sf/compmicro-ndutils-env:v${RELEASE_VERSION}
Or to run a bash shell in Apptainer:
apptainer exec docker://ghcr.io/czbiohub-sf/compmicro-ndutils-env:$v{RELEASE_VERSION} bash
We welcome contributions! Please see the Contributing guide