Pipeline Web Start

Pipeline Web Start (PWS) allows users to start and run the LONI Pipeline application from a web browser without installation. Users who choose this application will have access to all of the functions and features included in the downloadable version. PWS is accessible via an anonymous guest login or user-authentication to connect to remote Pipeline servers.

Alternatively, you can download the installer for the LONI Pipeline desktop application here. Desktop application and web start have the same features.

Click here to launch the Pipeline Web Start

Once the the JNLP file is downloaded, please double-click the file to launch the program.

The examples below will launch the PWS client, load specific predefined workflow protocols, and submit workflows to a dedicated LONI Pipeline server using guest privileges.

Neuro Imaging

AIR: Automated Image Registration
SVPASEG: Sub-Volume Probabilistic Atlas Segmentation

Bioinformatics and Genomics

MAQ, SAMTools, Bowtie (Integrated)
miBLAST: Basic Local Alignment Search Tool


  • Java version 7 or higher is required. The latest Java is recommended.
  • On Mac, FireFox browser is required. And please make sure in your Mac OSX settings, you allow apps downloaded from anywhere. Click here for more information.
  • Once the the JNLP file is downloaded, you may have to double-click the file if it doesn’t start automatically.
  • You have to allow access when it asks for permission to run on your computer.
  • You can launch any public accessible workflow with this format: http://users.loni.usc.edu/~pipeline/serverlib/jnlp_writer.php?url=[URL_TO_WORKFLOW]&server=[SERVER_NAME]&execute=true For more information, please check instructions for setting up Pipeline Web Start.

For more information on the LONI Pipeline application, please check our Quick Start Guide and User Guide.

Want to host Pipeline Web Start on your server? Instructions for setting up Pipeline Web Start on your server.


I get “pipeline.jnlp can’t be opened because it is from an unidentified developer.” message when trying to run Pipeline Web Start on Mac OSX, how can I fix this?

It is likely that your OS X’s GateKeeper prevents you from running LONI Pipeline. Open System Preferences and click on “Security & Privacy” icon. Unlock the lock in case it is locked and select “Anywhere” option. Now try to open LONI Pipeline package again and installation should work. After the Pipeline installation is done, you can change the Gatekeeper option to previously selected value. For more information, please refer to Apple’s documentation.