• Test GH Page: https://michaelakridge-noaa.github.io/container-images/

These are a collection of container images to provide standardized environments for Python and R computing built off the Rocker, Pangeo and Jupyter base images. This repo holds the (mostly) stable docker stack for specific pipelines used in Fisheries. Why use a container? The main reason is that geospatial, bioinformatics, and TMB/INLA environments can be hard to get working right. Using a Docker image means you use a stable environment. 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.

There are many other images in the images folder that are experimental in nature. There are also experimental images in the branches.

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
Specialized images
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

• 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.

The core stack is credited to the work of Luis Lopez (NASA) who developed the NASA Openscapes Python image used in countless workshops on cloud-computing with NASA Earth Data. Subsequently the NASA Openscapes mentor cloud-infrastructure Slack group and weekly co-work sessions plugged away at the problem of helping users 'fledge' off the Openscapes JupyterHub, which involved creating images that were more versitile. Carl Boettiger (Rocker, UC Berkeley) and Eli Holmes (NOAA Fisheries) took on different aspects of this. The GitHub Action tooling is curtesy of Carl. Yuvi Panda (Jupyter, 2i2c) was also very helpful in desiging the 'scaffolding' in the images that helps them be robust and versitile.

If your JupyterHub has this option:

• Click on the 'Bring your own image' radio button at bottom
• Paste in url to your image (or any other image)
• You will find the urls in the right nav bar under 'Packages'
• Example ghcr.io/nmfs-opensci/jupyter-base-notebook:latest

Should work out of the box. Put the url to the image whereever you would use images.

docker run -p 8888:8888 ghcr.io/nmfs-opensci/jupyter-base-notebook:latest

On a Mac M2+ with Rosetta emulation turned on in the Docker Desktop settings.

docker run --platform linux/amd64 -p 8888:8888 ghcr.io/nmfs-opensci/jupyter-base-notebook:latest

In the terminal look for something like and put that in a browser.

http://127.0.0.1:8888/lab?token=6d45c7d88aba92a815647c

Should work out of the box. Copy the Dockerfile into a repo and put the Dockerfile in the base or in a folder called binder. Then put this in a browser. Note many of the Docker images are big and somewhat hairy to build. This might not work in binder.

https://mybinder.org/v2/gh/user-name/reponame/main

See https://github.com/MichaelAkridge-NOAA/Open-Science-Codespaces

Still working to streamline this.

https://github.com/indigo-dc/udocker

Installation in the Jupyter notebook

%%shell
pip install udocker
udocker --allow-root install
udocker --allow-root run -p 127.0.0.1:8888:8888 -v -e ghcr.io/nmfs-opensci/jupyter-base-notebook:latest

All code used in the images is under open licenses. Some is copy-left which means if you modify their code (we don't), you need to also provide your source code. The Dockerfile code is released under Apache 2.0, a very permissive open source license which does not require that you make you own modifications open. See the README.md files for the licenses for specific code used in the Docker files.

• The Dockerfiles are released under Apache 2.0.

• jupyterhub : Modified BSD License

• juptyerlab: Open license

• Openscapes base Python image: MIT

• Pangeo Docker Stack: MIT

• Python: Zero clause BSD

• Openscapes base rocker image: MIT

• Rocker Docker Stack: GPL-2

• R: GPL-2, GPL-3

• RStudio Server: GPL-3

• conda and mamba solvers: are open source projects with 3-clause BSD license. Anaconda is not used in these images nor are the Anaconda repositories.

This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project content is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.

Or this? https://stackoverflow.com/questions/62820498/how-to-connect-google-colab-with-localhost-running-docker-image

port forwarding https://biplobsd.me/blogs/view/run-swirl-open-source-search-engine-on-google-colab.md