What version of Java do I need to run the LONI Pipeline?
The Pipeline requires Sun Microsystems’ Java 6 (JRE 1.6) or higher to run. To find out which Java version you have: in Windows, click Start-> Run… and type cmd and hit OK, then type java -version; in Linux/UNIX/Mac, under terminal, type java -version. Please note, other varieties of Java (which is not Java HotSpot distributed by Sun Microsystems) is not tested and LONI Pipeline may not work properly.
What happens if I get an ‘Incompatible Versions’ error when I try to connect to a Pipeline server?
Your version of the client is out of sync with the version the server is running. Download the latest version of the client and try connecting again. If you still receive the error message and you’re sure you have the latest version of the client, the server is probably running an older version of the Pipeline. In this case, contact the server administrator and ask them to update to the latest version of the Pipeline server.
How can I get access to the LONI Pipeline server?
It is a two-step process. First, if you don’t have a LONI account, fill out the LONI account application, which lets you download LONI software (including the LONI Pipeline), and post on the LONI forums. Second, if you need to connect to LONI Pipeline crainum server, you need to fill out the application form here. Note that you need to login with your LONI account in the first step. If you have any questions regarding account application, email us at pipeline@loni.ucla.edu.
How can I change my LONI Pipeline account’s password?
You can go to http://password.loni.ucla.edu to do so.
I think I’ve found a bug! How can I tell you guys?
You can file a bug report through the Pipeline client. Select Help -> Report a Bug from the top menu bar. If desired, fill out the optional fields for name, email and server username. You can also attach the workflow being processed and enter in any details about the bug.
What license is the LONI Pipeline released under?
Pipeline is released under the LONI license. You can view a comparison of the LONI License with other licenses as well.
Who funded development of the LONI Pipeline?
A list of funding agencies can be found here.
May I use the Pipeline client to execute workflows on my own computer?
Yes, in describing a module definition, simply specify the path of the executable to point to a local copy.
Is it necessary to write shell script wrappers for executable programs in order to describe these executables as Pipeline modules?
The pipeline environment does not require any modifications, rebuilds, redeployments of existent tools which provide a well-defined command-line executable invocation syntax. However, sometimes it may be helpful or necessary to wrap executable tools via external shell scripts (e.g., tcsh, csh, bash, etc.) Examples of these situations include:
* instances of command-line executable tools that have a well-defined invocation syntax, however, output implicit number, types and formats of results/data that can not be inferred a priori e.g. VolumeMultipleRegression tool.
* tools that require customized environmental variable settings, system controls or job-submission parameter settings (e.g., SPM, FSL/FEAT, etc.)
How I acknowledge my use of the Pipeline in my paper/publication?
Please refer to Acknowledgments and Credits page.
How can I provide feedback, make feature requests, or obtain help with the software?
If you want to make feature requests or need some technical help with the software that is not addressed in the user guide or server setup guide, you can check out our forums. You can do keyword search, and if you could not find answer, you can post your questions there. We will get back to you as quickly as we can.
May I package my workflows as part of a tool and distribute to others?
Once a workflow has been constructed, it can be saved as a .pipe file, which can be sent to collaborators. If specific servers are being accessed, privileges must exist for the user to connect to the server.
How do I disseminate my new computations tool and a corresponding Pipeline wrapper to the community?
Once you have constructed a new module definition, you may submit it for addition to the LONI pipeline server by emailing it to pipeline@loni.ucla.edu for approval and distribution through the LONI server.
If my executable has a GUI, how can I view it locally while the process is running remotely through a Pipeline server?
There are several steps that need to be carried out in order to accomplish this. In particular, you need to run an X server on your local machine, write a wrapper script to properly set up the DISPLAY environmental variable prior to running the executable, and specify that the job should be submitted to a node with external network access. The details can be found in the User Guide Advanced Topics.
