labkeyDocker

Labkey as a docker container

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

Installation

Prepare

• Install docker
• create a user labkey with docker privileges

   sudo adduser labkey
   sudo usermod -G docker labkey

• clone the software

   sudo su labkey
   cd
   git clone https://git0.fmf.uni-lj.si/studen/labkeyDocker.git

Database

Set path as POSTGRES_DIR in labkeyDocker/bin/env.sh, see below. If you don't have an existing database, it is enough to create the directory PGPASS from env.sh and postgresql container will create one.

EXPERT USE: To use existing database, make sure the version of the database match the container. Container versions are set in corresponding Dockerfiles, check the one COMPOSE in env.sh points to. Adjust PGPASS and password in env.sh and labkey.xml accordingly.

Check if database runs:

   labkeyDocker/bin/startPGonly.sh
   docker logs config-labkey-db-1
   labkeyDocker/bin/stopLabkey.sh

Files and external modules for LabKey

The files and externalModules locations are set in bin/env.sh, see bin/env.sh.sample:

   export EXTERNAL_MODULES=$HOME/externalModules
   export LABKEY_FILES=/data/labkey/files

Install LabKey binaries

Copy target binaries from LabKey or legacy repository to $HOME/packages. Uninstall and (re)install target binaries:

labkeyDocker/bin/uninstallLabkey.sh
labkeyDocker/bin/installLabkey.sh X

Adjust system properties

Copy labkeyDocker/bin/env.sh.sample to labkeyDocker/bin/env.sh and update enviorment variables:

• POSTGRES_DIR for location of database (on host system)
• set a secret PGPASS, should match the one used in database creation if database already exists
• set links to resources: EXTERNAL_MODULES, LABKEY_FILES
• both EXTERNAL_MODULES as well as LABKEY_FILES should be owned by labkey user.
• check DOCKERCOMPOSE, normally default docker compose is OK, but older docker version shipped compose separately as docker-compose.
• check that the COMPOSE points to the right .yaml file, where versions of labkey and compose match.
• for running behind SSL, hidden compose files are available, where access ports (8080, 8443) are not shared by the host. Use a reverse proxy, like this one to terminate SSL connection.

Setup labkey (labkey.xml)

Copy labkeyDocker/tomcat/conf/Catalina/localhost/labkey.xml.temp to labkey.xml in the same directory.

• set the same value as env.sh:PGPASS as password in labkey.xml

EXPERT USE: In labkey.xml one can adjust the postgresl ports and/or server if other than dedicated server is used.

Docker will also map labkeyDocker/tomcat/bin/setenv.sh to container space, which gives some global settings to the tomcat engine of LabKey.

EXPERT USE: In setenv.sh one can adjust java settings, for example add-exports to expose internal Java implementations, ie. for direct WebSocket use.

Start containers

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

• 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:8080/labkey. Check output of inidividual components by:

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

Add libraries to R

The appropriate Dockerfile (see section on prebuilt images below) should add typicall libraries to container. Should you find a further library you should need, contact me or update your dockerfile similarly to examples in Dockerfile21.

Pre-building images

In the latest version, images can be pre-built using docker hub as a repository for such images lacking adaptation to individual working environment.

To create such images, do

$ docker build -f config/web/Dockerfile21 -t andrejstuden/nix:x21 config/web
$ docker login -u andrejstuden docker.io
$ docker push andrejstuden/nix:x21