Resources for installing OHDSI ATLAS using Docker containers.
Follow these instructions for preparing the PostgreSQL database.
In either a Linux or a WSL terminal:
-
Install Java 8
-
Install Apache Maven
-
Set the environment variable MAVEN_OPTS to prevent out of memory errors with
MAVEN_OPTS="-Xmx 1024"
-
Install Git
-
Install Git Large File Systems (Git-LFS) with
sudo apt update sudo apt install git-lfs
-
Create a new directory
~/git/OHDSI
andcd
to it. -
Download the latest version of WebAPI with
git clone https://github.com/OHDSI/WebAPI.git git checkout refs/tags/v2.11.1
-
Customize the WebAPI
settings.xml
file with the details of the PostgreSQL database as specified here. -
From the directory created by the
git clone
operation, (like~/git/ohdsi/WebAPI
), build the .war file withmvn clean package -DskipUnitTests -DskipITtests -s WebAPIConfig/settings.xml -P webapi-postgresql
-
Upload the
~/git/OHDSI/WebAPI/target/WebAPI.war
file to the DBMIAtlasInstallation
repo.
We'll run Atlas in a Docker container.
-
Install Docker.
-
Install Git.
-
In a convenient subdirectory (perhaps
C:\Git\OHDSI
) clone theAtlasInstallation
repo:git clone https://github.com/DBMI/AtlasInstallation.git
-
In the
C:\Git\OHDSI\AtlasInstallation
directory, build the Docker container withdocker build . -t atlas-installation
-
Run the Docker image with
docker run -d -p 8080:8080 atlas-installation
-
View the Atlas start page at