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FlowJo Commandline is an architecture within the FlowJo software intended for “hands free” processing. The syntax and creation of these commands can be laborious and error prone – tabs, spaces, quotes can make or break the execution. To reduce the uncertainties, using CommanJo allows you to compose these with a few clicks of your mouse.

To launch CommanJo – first start the Diagnostic tool, and then click the “CJ” button corresponding to the installation of FlowJo you wish to use:




This brings up the main a CJ panel:


The two fields for Executable and Preferences panel are already filled out for your convenience, but you can override them by clicking a corresponding “Choose” button and navigating to a different one.

The three fields in the upper-left corner of the interface, “Drag data / workspace / output”, accept drag-and-drop gestures:

  • drag your data folder from your file system to the “Drag Data folder here” field.
  • drag your WSP/T file to the “Drag Workspace/Template..” field.
  • set your desired Output folder by dragging it onto the “Output Folder” field.

The series of checkboxes on the left side correspond to different macro options you can enable for command line execution:

  • “Save” option will process a WSPT file and create a WSP file in the output folder.
  • “Save as ACS” option is similar to above, but compacts the FCS files as well.
  • “Compensate” option will attempt to see if any samples from your input data seem like single-stain-controls. This doesn’t work for all data, so you alternatively can feed a “matrix” file on the right side of the interface.
  • “Show All Graphs” button will dump all gates in the workspace window as PNG images of their graph spec (typically the axes used to create a child gate.)  These will be placed in the specified Output Folder.
  • “Keep Cache Directory” is useful if you access remote data.
  • “Run Batches” is an option needed for WSP input files.
  • “Show Engine Output” creates an XML file with details about the session – very useful if you keep track of execution times, memory consumption, cache use, etc.
  • “Show Cache State” – additional details about cache.
  • “Verbose” – increases the amount of spam in the Console output
  • “Show Sample Quality” will perform the parametric scan of data vs time and report on deviation.
  • “Create Unique Identifier” if you are iterating over equivalent data and don’t want to over-write your outputs in every run, check this box 😉
  • “Matrix” (on the right hand side) allows you to specify a matrix XML file created by FlowJo Vx. This is useful because not all data works 100% smoothly with autocompensation (we’re working on it.)