There are two ways to configure programming environment and execute simulation procedure:
install multiple R packages and dependencies from github, it may take 5-30 mins.
install Docker first and download simpipe Docker image from DockerHub. All manipulations in R can be done by a lightweight simpipe2doker package.
The first way to configure your programming environment is to install all of the packages and necessary dependencies
You can install the development version of simutils, simmethods and simpipe from GitHub by:
# install.packages("devtools")
devtools::install_github("duohongrui/simutils")
devtools::install_github("duohongrui/simmethods")
devtools::install_github("duohongrui/simpipe")If you want to use simpipe to simulate datasets with trajectory information, please install tislingshot first by:
devtools::install_github("dynverse/ti_slingshot/package/")We provide another way for users to configure your environment by Docker. To achieve the interaction between Docker and R environment, we build a lightweight R package simpipe2docker which is used for calling commands in terminal to link Docker and R. It is more easier to manipulate and suitable for different operation systems and R versions, avoiding complex configurations in various environments.
If you have not installed official Docker Desktop, please click here and follow the instructions to install it.
The version of Docker Desktop for Apple Chip is available
After installing Docker, start Docker service, open an R session and type dynwrap::test_docker_installation(detailed = TRUE):
dynwrap::test_docker_installation(detailed = TRUE)
✔ Docker is installed
✔ Docker daemon is running
✔ Docker is at correct version (>1.0): 1.41
✔ Docker is in linux mode
✔ Docker can pull images
✔ Docker can run image
✔ Docker can mount temporary volumes
✔ Docker test successful -----------------------------------------------------------------
[1] TRUEIf it is TRUE in the result, that means Docker is successfully installed.
Use babelwhale::pull_container("duohongrui/simpipe") command to pull simpipe Docker image in R (it will take 3-10 mins):
# install.packages("babelwhale")
babelwhale::pull_container("duohongrui/simpipe")Once the image has been downloaded, check the image list:
babelwhale::list_docker_images("duohongrui/simpipe")
# A tibble: 0 × 7
# ℹ 7 variables: ID <chr>, Repository <chr>, Tag <chr>, Digest <chr>,
# CreatedSince <chr>, CreatedAt <chr>, Size <chr>Get the simpipe2docker package from github by:
devtools::install_github("duohongrui/simpipe2docker")Load the package and check whether it is installed successfully:
library(simpipe2docker)Until now, you have successfully established the programming environment 👍👍👍. Go to the next page.👈️