In dynverse/dyngen: A Multi-Modal Simulator for Spearheading Single-Cell Omics Analyses

To ensure reproducibility, you can run dyngen in a docker container. dynverse/dyngen contains all necessary packages to run dyngen from start to finish. Ideally, you would take a look at the latest tag published on docker hub and replace any mentions of dynverse/dyngen with dynverse/dyngen:<latest digest>, to make sure you're always using the exact same version of dyngen.

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 dynverse/dyngen

Keep this window open, and open up a browser and go to 127.0.0.1:8787. Open up the file getting_started.R for a small example on how to run a dyngen simulation.

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 in the rstudio home folder
  # so you will see it right away when rstudio starts
  -v `pwd`:/home/rstudio/workdir \

  # specify which container to run
  dynverse/dyngen

Update the container

If a newer version of the container has been released, you can update it by running the following command.

docker pull dynverse/dyngen

Building the container

To build this docker container from scratch, run the following command.

docker build -t dynverse/dyngen -f docker/Dockerfile .

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

dynverse/dyngen documentation built on Oct. 29, 2022, 10:12 a.m.