Personal tools
  • We're Hiring!

You are here: Home Documentation Previous versions OME Server System Administration Executing Analysis Chains

Executing Analysis Chains

Both the web-ui and ome can be used to execute chains although the command-line approach is preferred since it provides more verbose output reporting and allows for specifying user inputs.

The following command executes the Find spots analysis chain against the dataset "Inverse Image". Use the web-ui's search facility to find analysis chains and datasets of interest.

ome execute -d "Inverse Image" -a "Find spots" -s
User Inputs:
Find spots.Parameters:
  New or existing? [N]/E  n
  Attribute #1
    ThresholdValue: 150
    ThresholdType: Absolute
    MinimumSpotVolume: 10
    Channel: 0
    TimeStop: 0
    TimeStart: 0
  Attribute #2
    FadeSpotsTheT: \d
Executing Analysis Chain `Find spots`
         1/4: [IN PROGRESS] Currently Start Execution of Analysis Chain
         4/4: [IN PROGRESS] Currently Executing `Find spots`
      4/4: [FINISHED] Currently

Several flags can optionally be passed into ome execute. I recommend the Reuse Results flag be set (-f parameter) if there is a chance that the analysis modules' underlying code (whether implemented as a command-line tool, in Matlab, or in Perl) was changed from the last time the analysis chain was called.

Use the web-ui to view the results of the analysis chain execution.

Executing MATLAB based Analysis Chains

If your analysis chain contains Matlab based Analysis Modules, there are other issues you need to be aware of -- mainly stemming from the MATLAB licensing system. For more information please read the guide on installing the Matlab connector and documentation about the Matlab Handler.

Document Actions