labkeyDocker

Labkey as a docker container

This git project contains everything required to start labkey as a docker container.

Installation

Prepare

• Install docker and docker-compose
• create a user labkey with docker privileges

sudo adduser labkey
sudo usermod -G docker labkey

• clone the software directly into home

sudo su labkey
cd
git init .
git remote add origin <repository-url>
git pull origin master

• run bin/installLabkey.sh 22.3 to unzip the enclosed LabKey binary code and make appropriate links.
• copy bin/env.sh.sample to bin/env.sh and set a secret $PGPASS, other settings are probably OK, check $DOCKERCOMPOSE
• set the same value as password in labkey/labkey.xml
  

Start containers

Run bin/startLabkey.sh. This will do several things:

• Download PostgreSQL image and initialize a persistent database at ~/postgresl/data.
• Build a combined tomcat/R image from a recent version of tomcat
• Copy and link files from home to the server
• Start the server

Check the installation

In principle, the service should be running at http://localhost:8443/labkey. Check output of inidividual components by:

  docker logs config-db-1
  docker logs config-web-1
  docker exec -it config-db-1 bash
  

Add ggplot2 to R

Connect to running instance of labkey:

docker exec -it config_labkey-web_1 bash

Start R:

R

In R, installggplot2 with dependencies:

install.packages('ggplot2', repos='http://cran.us.r-project.org', dependencies=TRUE)

Install ggpubr

For ggpubr, install cmake first. When in config_labkey-web_1 do:

apt update
apt install cmake

Then, in R:

install.packages('ggpubr')

Manage postgresql

Create ${POSTGRES_DIR} directory as user that will be running the container. If you have trouble with initial setup, the base can be reset by deleting everything under postgresql/data.

Expected errors

Errors of the type 500: Unexpected server error are common and related