No Description

Andrej Studen 8722064747 Adding option to set catalina in development mode 2 weeks ago
bin 66d57a17b4 Updating container name in startPGOnly 11 months ago
config 409e643460 Fixing R build in docker file 1 year ago
labkey bb26540f8d Updates for a smoother run, partcularly, files will be created with permissions identical to the user running the docker container, which is better for granulation 1 year ago
software 4356237ce1 initial import 3 years ago
tomcat8 8722064747 Adding option to set catalina in development mode 2 weeks ago
README.md 72f0be54fa Update 'README.md' 1 year ago
Re 08162045ca Adding README.md 3 years ago

README.md

Labkey as a docker container

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

Installation

Prepare

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