# Labkey as a docker container

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

## Installation

### Prepare

- Install [`docker`][docker] and [`docker-compose`][dockerCompose]
- create a user `labkey` with `docker` privileges

```bash
sudo adduser labkey
sudo usermod -G docker labkey
```

- clone the software directly into home

```bash
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` 

### Permissions

To run as non-root user labkey, files should have the proper permissions. I believe that starting from scratch, 
the neccesary files will be created with appropriate permissions. If using an old implementation or in case of troubles, the following directories should be owned by labkey:labkey on host machine:

```bash
~/software/src/LabKey22.3.2-3-community/*
~/labkey/externalModules
~/labkey/files
```

### 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:
  
```bash
  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:

```bash
docker exec -it config_labkey-web_1 bash
```

Start R:

```bash
R
```

In R, install`ggplot2` with dependencies:

```R
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:
```bash
apt update
apt install cmake
```

Then, in R:
```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 
  
[docker]: https://docs.docker.com/engine/install/
[dockerCompose]: https://docs.docker.com/compose/install/