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:

   ```bash
   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