docker/README.md

In rcannood/GillespieSSA2: Gillespie's Stochastic Simulation Algorithm for Impatient People

Running GillespieSSA2 in a Docker container

rcannood/gillespiessa2 contains all necessary packages to run GillespieSSA2 from start to finish.

Running the container

To run the container, you can use the following command.

docker run --rm -p 127.0.0.1:8787:8787 -e DISABLE_AUTH=true -v `pwd`:/home/rstudio/workdir rcannood/gillespiessa2

Keep this window open, and open up a browser and go to 127.0.0.1:8787. Open up the file vignettes/an_introduction.Rmd or any of the other vignettes for a small example on how to run SSA simulations with GillespieSSA2.

The command can be dissected as follows.

docker run \

  # remove container after use
  --rm \

  # specify which port rstudio server uses
  -p 127.0.0.1:8787:8787 \

  # disable authentication because I'm lazy
  -e DISABLE_AUTH=true \

  # mount the current working directory to the rstudio home folder
  # so you can save results in the 'workdir' folder for later use
  -v `pwd`:/home/rstudio/workdir/ \

  # specify which container to run
  rcannood/gillespiessa2

Update the container

If a newer version of the container has been released, you can update it by running the following command.

docker pull rcannood/gillespiessa2

Building the container

To rebuild this docker container from scratch, run the following command with GillespieSSA2 (from the GillespieSSA2 folder, not the docker folder).

docker build -t rcannood/gillespiessa2 -f docker/Dockerfile --build-arg GITHUB_PAT=$GITHUB_PAT .

GITHUB_PAT should be an environment variable corresponding to the Personal Access Token created by following this tutorial.

rcannood/GillespieSSA2 documentation built on Jan. 26, 2023, 8:33 p.m.