NMFS Open Science Docker Stack
THE DOCKER STACK IS IN ACTIVE DESIGN and DEVELOPMENT
Beta release targeted for June 1, 2024.
These are a collection of container images to provide standardized environments for Python and R computing build off the Rocker, Pangeo and Jupyter base images. This repo holds the (mostly) stable docker stack for specific pipelines used in Fisheries. Our development and testing sandbox is here: nmfs-opensci/container-images which is our sandbox and development location. Why use a container? Watch this video from Yuvi Panda (Jupyter Project) video and read about the Rocker Project in the R Project Journal article by Carl Boettiger and Dirk Eddelbuettel.
Stable set of images
There are many other images in the images folder that are experimental in nature.
| Image | Description | Size | Link | Dockerfile |
|---|---|---|---|---|
| nmfs-opensci-python-base | Geospatial Python based on NASA Openscapes image | nmfs-opensci-python-base | Dockerfile | |
| py-rocket-base | Tidyverse based R image with Python | py-rocket-base | Dockerfile | |
| py-rocket-geospatial | Geospatial R and Python image | py-rocket-geospatial | Dockerfile | |
| arcgis | For using ArcGIS within Jupyter Lab | arcgis | Dockerfile | |
| coastwatch | CoastWatch Python + R | coastwatch | Dockerfile | |
| cmip6-cookbook | Tooling for working with CMIP6 climate simulations | cmip6-cookbook | Dockerfile | |
| echopype | Tooling for ocean sonar (acoustics) data processing | echopype | Dockerfile | |
| VAST | VAST with R 4.3.3 | vast | Dockerfile | |
| aomlomics-jh | NOAA AOML omics image for amplicon sequence processing workflow (adapted for JupyterHub deployment) | aomlomics-jh | Dockerfile |
Click on the image name in the table above for a current list of installed packages and versions
Design principles
- Python environment follows Pangeo images with micromamba installed as the solver and base and notebook environments. The Jupyter modules are installed in notebook environment and images will launch with the notebook activated, again following Pangeo design structure. Images that use Pangeo as base will have user jovyan and user home directory home/jovyan.
- R set-up follows Rocker’s environment design with the exception that the user home directory is home/jovyan so it plays nice with JupyterHub deployments. The user is rstudio however.
- When an image contains both R and Python, the base image is rocker and micromamba is installed along with the Pangeo environment structure. RStudio will use the Python environment in the notebook environment when Python is used from within RStudio.
- The images are designed to be deployable from JupyterHubs, Codespaces, GitPod, Colab, Binder, and on your computer via Docker or Podman. See instructions below.
- However, they are not terribly light-weight (large). Use the original Jupyter, Pangeo or Rocker images if you are looking for simple lightweight data science images.