docker/README.md

In ohdsi-studies/LegendT2dm: Large-Scale Evidence Generation and Evaluation in a Network of Databases

Docker Image for LegendT2DM

Instructions

• Open a terminal
• Clone LengedT2DM by typing git clone https://github.com/ohdsi-studies/LegendT2dm.git
• Go into the docker subfolder cd LengedT2DM/docker
• Run the container by using the auxiliary script Rscript run_docker.R. Please change the variables local_folder and gcloud_local_folder. If you are not using gcloud you can safely remove lines 5 and 15
• Open a tab in your preferred brower and type localhost:9001. This will open an Rstudio server instance running locally.
• Type the username and password. By default both are ohdsi. you can change that inside the run_docker.R
• Once in RStudio change the directory to /workdir/workdir
• Source testRun.R to confirm everything is working. If you are not using gcloud several paramteres need to be changed in that script to connect to an instance you are authorized to.

File Description

• Dockerfile: This file contains the steps performed to create the docker image on jdposa/legend_t2dm:0.4. The image is based on an image created by Odysseus Inc rocker/rstudio:4.0.5. This dockerfile contains the installation of libsodium an OS library required to run the R sodium package.
• build.R: Small R script to build the Dockerfile and create the docker image.
• install_renv_lock.R: Small R script to use the renv.lock file to create an R library that contains everything eneded for the study.
• install_additional_packages.R: Small R Script to install any additional packages besides what it is inside the renv.lock file. As of now includes a small package to ease the creation of teh conneciton string when using bigquery. Also it builds the LengedT2DM package programatically. If anyone needs to install any other dependency not covered in renv.lock, this is the space to do so.
• renv.lock: This is a copy of the file found in the main folder of this repo.
• run_docker.R: Small R script to download and run the Docker image creating a container named rstudio-ohdsi. This small script can be modified in a way that the user could mount a directory of their chosing and specify the forwarded port used to launch RStudio.
• testRun.R: This small R Script is meant to test the Docker container by running a small SQL against the Bigquery Public Synpuf dataset formatted as an OMOP-CDM v5.3.1

NOTE: To build the image the renv.lock file from the main folder needs to be copied to the docker folder.

ohdsi-studies/LegendT2dm documentation built on July 4, 2025, 8:25 p.m.