Collection of Jupyter notebooks to run landscape elevation models with a biodiversity flavour!
The notebooks rely on two main scientific software:
- badlands provided within the docker container below,
- circuitscape that will need to be downloaded in addition to the container
In addition, several libraries and scripts are required and have been packaged in a Docker container. So on top of the notebooks available in this repository it is recommended to download the following container:
Once you have installed Docker on your system, you can pull the image as follow:
docker pull geodels/gospl:bio
You can list all the images available on your system as follow:
docker images
An image can be deleted as follow:
docker rmi geodels/gospl
You can then start a docker container (an instance of an image):
docker run -d --name my_container -p 8888:8888 -v my_vol:/live/share geodels/gospl:bio
You can access the container via your browser at the following address: http://localhost:8888
It is also possible to ssh into the container as follow:
docker run -it -v my_vol:/live/share --entrypoint /bin/bash geodels/gospl:bio
You can list the containers currently existing on your machine by running:
docker ps -a
The -a means “all container”. The docker ps command only list running containers.
Docker containers can be stop (so that they do not use CPU or RAM resource):
docker stop my_container
They can also be deleted:
docker rm my_container
It’s a good idea to keep track of how many containers have been created as they can rapidly take a lot of space on your machine.
Kitematic is a program that provides a graphical user interface to the docker daemon and to Docker Hub.
The software is available for Windows, Mac OS X and Linux. Be aware that on linux the installation may differ depending on the distribution you are running.
- Download and Install Kitematic
- Open Kitematic and search for the tag corresponding to a specific the gospl version.
- Download the container by clicking on the create button.
You should now have a container appearing on the left side of your kitematic window.
The first thing to do now is to create a link between a local directory (A directory on your physical hard drive) and a volume directory inside the docker container. A volume is a special directory that can be accessed from outside the container. It is the location you will use to save your own results.
- Precipitation grids: download dataset from http://www.paleoclim.org and we use the variable Bio_12: Annual Precipitation [mm/year].
- Digital elevation grids: download dataset from https://www.ngdc.noaa.gov/mgg/global/ using the ETOPO1 Bedrock geotiff for example.