Download autobatch tutorial [MOV, 18.2MB]
Summary:
Auto-Batching is a feature which can be utilized when running flowjo in Command-Line Mode (CLI). CLI was developed to give the set of features necessitated by large volumes of data set that may need automated pre-processing prior to 'attended' analysis - pre-gating, compensation calculations, exporting gates to smaller FCS files, are some examples of tasks that fall into that category.
AutoBatch is best initiated from an existing template which has things like:
- dynamic live groups with group-owned-gates
- tables defined in the Table Editor
- layouts defined in the Layout Editor
AutoBatch in Table Editor:
- open an existing Table in your Table Editor. Click Edit menu >> Include in Batches.
- define an output for your table that gets written to disk. Click Batch button, then set the option for "File", pick a flavor & output destination, and hit "Save" and "Apply" buttons. This commits the autobatch settings to this particular table.
- notice the tables which were autobatch enabled, are listed in BOLD typeface.
AutoBatch in Layout Editor:
- open an existing layout, click Layout menu >> Include in Batches.
- Click Batch button and define some sort of File output (PDF, PPT etc.) and destination. Remember to hit "Save" and "Apply".
- notice autobatched layouts are listed in BOLD typeface.
AutoBatching file export/concatenation:
- this is initiated slightly differently from the above two, since there is no "batch" button.
- to autobatch the export or concatenation of UNGATED FCS files to csv/fcs data on disk, right-click the group definition at the top level, click Export/Concat. In the Export/Concat dialog select your destination (currently ignored, defaults to template location) and file flavor, as well as whether or not to concatenate the data. Lastly, check the "save in template" checkbox - this commits your actions to the template's memory.
- to autobatch the export or concatenation of GATED data (ex. "merge all my T cell gates into one CSV/FCS file"), right-click the group definition at that gate's level, then click Export/Concat. After this point the directions match the "ungated" export/concat.
Executing "AutoBatch" templates:
this requires either access to the command prompt or ability to generate and execute .bat (batch) files.
the command syntax follows:
c:\path\flowjo.exe c:\path\template.wspt c:\path\experiment1 -save -quit
where the flowjo exectuable (path + exe name) is called with four arguments: the input template (path + document name), the input data (path), and two optional arguments to save the executed work into a workspace file. The "-quit" argument is optional but recommended to free up any runaway RAM consumed by each batch :)