bushlab/rbiotools repository overview

This is a container with the following packages installed:

• R with RStudio
• readxl, knitr, rmdformats, magrittr, here, janitor, rms, broom, haven, car, GGally, tidymodels, broom.mixed, caret, ROCR, pROC, data.table, naniar, rsample, yardstick, gtsummary, ggpubr, robust, mice, HardyWeinberg, plm, mediation, tidyverse
• bcftools
• samtools
• htslib, including tabix and bgzip
• plink and plink2
• SeqArray

⁠Running the container

First, run:

hostname 

to find the domain through which you can access the container via port mapping.

For this document, assume that the output of the above command is localhost.

⁠The Docker Run command

docker run --rm -p 8787:8787 -e PASSWORD=password -v $(pwd):/home/rstudio/mount_dir -e USERID=$(id -u) -e GROUPID=$(id -g) bushlab/rbiotools:v1.0

⁠What this does:

Port Mapping

-p 8787:8787

This will initialize RStudio, and will map your domain's port 8787 to the container's port 8787, which can be accessed at the following url:

localhost:8787

Volume Mounting

-v $(pwd):/home/rstudio/mountdir

This mounts the present working directory from which you run the Docker run command to /home/rstudio/mount_dir within the container.

Permission Setting

 -e USERID=$(id -u) -e GROUPID=$(id -g)

This sets the environment variables USERID and GROUPID within the container to the USERID and GROUPID of the user running the Docker run command, to prevent issues with file permissions within mounted directories after exiting the container.

⁠Accessing RStudio

Navigate to

# Note that you need to replace `localhost` with the output of your `hostname` command.
localhost:8787

Username: rstudio

Password: password

The entry point for this container is /home/rstudio.

⁠Biotools

samtools, bcftools, htslib, tabix and bgzip have been installed in the /opt directory. Their absolute binary file locations have been appended to the .bashrc file at /home/rstudio, which means that these tools can be run on the bash shell within the RStudio instance.

Similarly, plink and plink2 have been installed at /home/rstudio, and can be similarly accessed from the command line.