Prerequisite

You need a running installation of docker, docker-compose. Make sure you can call docker commands without sudo.

When you are working in a windows home edition environment you are forced to use the docker toolbox instead. The use of the iLCM based on docker-Toolbox is working but not recommend due to limitations caused by third-party-software (virtualbox).

Download Install File

Please download the right file for your operating system from http://ilcm.informatik.uni-leipzig.de/software/download/ and unzip it.

Install Script

Linux/Mac

Open a terminal inside the unziped directory.

$ cd /home/user/downloads/Install_ilcm_linux

Then just run:

$ sh install.sh

Windows 10 Pro

Please open Windows Powershell as administrator (rightclick run as administrator). Change the current directory to the directory of the unziped installation file. Run:

$ .\install.bat

Windows others (docker Toolbox)

Open the docker quickstart terminal. Go to the unziped directory.

$ cd C:/Users/User/Downloads/Install_ilcm_toolbox

Then just run:

$ sh install.sh

Change virtualbox settings

In order to make the iLCM work using docker Toolbox, we need to change the default settings of the created boottodocker image in virtualbox. Therefor open virtualbox virtualbox and stop the running instance of the image called “default”. Then we need to change the settings of “default” giving it more ram and cpu-cores. more RAM more cores Having done this, you can close virtualbox again and either re-open the docker quickstart terminal or type in the open docker quickstart terminal:

$ docker-machine restart default

Start Services

Once the installation was successfull you can start the iLCM without using the install bash script. You need to go to the directory, where the docker-compose.yml file is located. Open in a terminal here. Type:

$ docker-compose up -d

#Check Logs of Containers You can check the logs of the containers with:

$ docker logs tmca_db_1

Stop Services

Ensure you are in the directory, where the docker-compose.yml file is located in.

$ docker-compose stop

Access Results

In your home directory there is a directory called “iLCM”. In here we save the results, logs and other usefull files created while using the iLCM. You will also find the configuration files for solr and mariadb if you are interested in manipulating them for your requirements. Under iLCM/data/r/collections/results you can access the results created inside your iLCM isntance.

Update Images

New images can be obtained using:

$ docker pull ckahmann/ilcm_r:latest
$ docker pull ckahmann/rstudio:latest

You can check the latest releases on https://hub.docker.com/r/ckahmann/.

Use iLCM

When you have successfully installed the services, you can access them using a browser. The services are attainable at different ports.

  • Shiny iLCM: http://localhost:3839
  • Rstudio Server: http://localhost:3840
  • myphpadmin: http://localhost:3841
  • solr: http://localhost:3842

If you are using the toolbox, you need to replace ‘localhost’ with ‘192.168.99.100’.

iLCM

The ShinyApp is the main tool of using the iLCM. Therfor you can access a Shiny Server, which has a instance of the latest ShinyApp running. You need to open a browser window (tested on Chrome and Firefox) and go to: http://localhost:3839.

RStudio Server + ShinyApp

The ShinyApp can also be used inside an RStudio-Server environment under http://localhost:3840. Using the Rstudio-Server it’s possible to make live changes to the Code of the app or isntantly use the results created with the implemented scripts of the iLCM for other purposes.

For opening the ShinyApp inside the RStudio-Server please check the directory called “ShinyApp”. In this directory you will find a file called “app.R”. Once you have clicked on this file, in the top part a button called “Run App” will appear. After clicking this button and ensuring that your brwoser allows Popups from this site, you can start using the iLCM.

The Login for the RStudio-Server can be changed in the docker-compose.yml file.

environment:
        - USER=User
        - PASSWORD=Password

myphpadmin

myphpadmin is a service that lets you watch and manipulate the status of the used maria database. The default login for myphpadmin can be set in the docker-compose.yml file. The default login is:

  • User: myphpadmin
  • Password:myphpadmin

solr admin

Solr is our full text search engine. You can access the solr admin view using http://localhost:3842.

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