dsblab/cellbasedmodels repository overview

⁠cellbasedmodels docker

The dockerfile makes an image that contains a set of relevant packages for the use with CellBasedModels.jl⁠. A list can be seen in environment.yaml.

⁠Running the image

⁠Interactive Shell

Start the container in interactive format.

docker run -it \
    --mount type=bind,source="$(pwd)",target=/home \
    dsblab/cellbasedmodels:v0.1.0 julia

⁠Script

To execute directly a bash script simply

docker run \
    --mount type=bind,source="$(pwd)",target=/home \
    dsblab/cellbasedmodels:v0.1.0 /bin/bash -c "<bash_script.sh>"

and a julia script

docker run \
    --mount type=bind,source="$(pwd)",target=/home \
    dsblab/cellbasedmodels:v0.1.0 /bin/bash -c "julia <julia_script.py>"

⁠Jupyter lab

If you want to work interactively with a jupyter notebook.

docker run -it \
    -p 8888:8888 \
    --mount type=bind,source="$(pwd)",target=/home \
    dsblab/cellbasedmodels:v0.1.0

You can then view the Jupyter Notebook by opening http://localhost:8888 in your browser, or http://<DOCKER-MACHINE-IP>:8888 if you are using a Docker.