Setting up on your computer - R users

Running locally

If you are set up locally to run R and have tidyverse installed, then for most of the tutorials, you only need to install earthdatalogin and terra with

devtools::install_github("boettiger-lab/earthdatalogin")
install.packages("terra")

RStudio should alert you if there are other packages that you need to install.

Running from Posit Cloud

The standard Posit Cloud has most of the packages you will need. For most of the tutorials, you only need to install earthdatalogin and terra with

devtools::install_github("boettiger-lab/earthdatalogin")
install.packages("terra")

Running from a Docker file

If you don’t have RStudio or R installed, the easiest way to run the R tutorials locally is to use the Docker container py-rocket-geospatial; this is the environment that is being used in the JupyterHub. You’ll need containerization software such as Docker Desktop or Podman installed.

Start the docker image

Make sure Docker or Podman is running (open the Desktop application), then run the container:

Windows, Linux or Intel-chip Mac:

docker run -p 8888:8888  --cap-add SYS_PTRACE --security-opt seccomp=unconfined  ghcr.io/nmfs-opensci/container-images/py-rocket-geospatial:latest

Apple-chip Mac (probably will not work):

docker run -p 8888:8888 --platform linux/amd64  --cap-add SYS_PTRACE --security-opt seccomp=unconfined  ghcr.io/nmfs-opensci/container-images/py-rocket-geospatial:latest

Tip

If you’re using Podman, simply replace docker with podman in this command and any that follow.

After docker run there will be a long printout in the terminal window, you will see instructions for how to access the server (To access the server...). Copy and paste either of the URLs into a web browser. You should be greeted with a JupyterLab dashboard as in the live demo.

Clone the tutorials

Clone and then cd into the repo. Open a terminal and run

cd ~
git clone https://github.com/nmfs-opensci/EDMW-3B-tutorials

The Python tutorials are in the tutorials/python directory.

Connect your local files to image

Clone and then cd into the repo. Open a terminal and run

git clone https://github.com/nmfs-opensci/EDMW-3B-tutorials
cd EDMW-3B-tutorials

Windows, Linux or Intel-chip Mac:

docker run -p 8888:8888  --cap-add SYS_PTRACE --security-opt seccomp=unconfined -v /$(pwd):/home/jovyan/ ghcr.io/nmfs-opensci/container-images/py-rocket-geospatial:latest