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Using sCCIgen Docker image

Source: vignettes/docker.Rmd
docker.Rmd

We have created a Docker image that will display an RStudio window on your local browser where you can run the sCCIgen commands and use the interactive Shiny app.

Clone the Docker image

Run the following command in your bash terminal:

docker pull sccigenpackage/sccigen:latest

Place the files that you will use for the simulation into a known folder

We need to create a directory to place the expression data and other files used while working with sCCIgen.

You can use terminal command or your preferred method to create a new directory. If you already have a previous data directory, skip this step.

mkdir Documents/my_wd

Start the image

Run the following command to start the interactive sCCIgen image, the -v option will connect your data folder with the docker working directory to read files while running RStudio.

docker run -e PASSWORD=mypassword -p 8787:8787 -v /path/on/host:/home/rstudio/ sccigenpackage/sccigen

Note that you need to replace the “/path/on/host” with the absolute path to your data directory that contains the files you want the docker image to have access to (e.g. Users/joselynchavez/Documents/my_wd/:/home/rstudio/).

Open your preferred browser

Once the image starts running, open your preferred browser and look for this address:

localhost:8787

Use the following credentials to sign in:

user: rstudio password: mypassword

Load sCCIgen

Use the R commands to start running simulations with sCCIgen.