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A lightweight Java GUI to launch ProtProtocol images


This Java tool provides a simple graphical user interface to install and launch ProtProtocol images.

ProtProtocol images are shipped as Docker containers that contain a complete analysis environment for common proteomics bioinformatics workflows. Since Docker containers are light-weight virtual machines, all required software tools are installed by simply downloading the image.

We currently provide the following ProtProtocol images:

  • IsoProt: This protocol supports the analysis of isobarically-labelled (TMT/iTRAQ) datasets starting from the identification of the spectra to the final statistical and differential expression analysis.



  • docker-launcher requires Java to be installed. You can download Java from
  • You also need to have Docker installed on your system. For help with this step see our docker installation manual
  • Download the current version from the releases.
  • Unpack the zip file to any directory
  • Simply launch the docker-launcher-[VERSION].jar file (double click or use `java -jar /path/to/docker-launcher-[VERSION].jar)


Version 0.5

  • Updated to new ProtProtocols docker hub name
  • Added alerts for all critical errors

Version 0.4

  • Available protocol image versions are automatically detected based on the GitHub tag versions.
  • Added controls to set input and output directory separately
  • Re-styled application
  • Added icon

Version 0.3

  • Added support to launch image when Windows drive sharing fails
  • Detects if a new version is available for download (necessary as protocol versions are hard-coded)
  • Detects IP address of docker host when running Docker Toolbox


  • Fixed bug that prevented image download in Windows 10
  • Fixed bug that prevented file sharing to work with Docker Toolbox

Version 0.2

  • Added functionality to select which image version to download and / or update


This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme under grant agreement No 788042.