![]() FlowJo executes the template using this data, performing the specified analysis determined by the template.ģ) -saveAs /Users/username/Desktop/CommandLineDemo/p Points FlowJo to the CommandLineDemo folder where the fcs files to be analyzed are stored. Open the TCellSubsets Template which is saved to a folder on the desktop (for more information on creating a template, please see this page). Those tasks are.ġ) /Users/mike/Desktop/CommandLineDemo/pt Which invokes FlowJo Version 10 (the -W and -g options indicate to wait for the application to exit before proceeding, and to not bring the application to the foreground when executing), as described above, and passes everything after –args to FlowJo as a list of tasks to perform. Open -W -g -a /Applications/FlowJo.app/ -args Note that in this case, quotes (“”) are unnecessary as none of the files nor folders contain spaces.įigure 2. Open -W -g -a /Applications/FlowJo.app/ -args /Users/mike/Desktop/CommandLineDemo/pt /Users/mike/Desktop/CommandLineDemo/ -saveAs /Users/mike/Desktop/CommandLineDemo/p -outputFolder /Users/mike/Desktop/CommandLineDemo/Output To invoke command line on the Mac, open the application “Terminal” and enter the commands that will be passed to FlowJo: bat file to the DOS command shell (cmd.exe). bat file referencing a workspace to open using command line. bat file to automate analysis of FCS files.įigure 1. One can similarly reference data folders and templates in this. We then simply go to Start/Run/cmd.exe to open the DOS Command Shell, and can drag and drop this bat file into the shell (Figure 1B). “C:Program FilesFlowJo VxFlowJo_V10.exe” “C:Documents and SettingsVince XPDesktop20120906 vX10_0_03.wsp”Īnd saved it as “FJ vX 10 0 3 commandline.bat” (Figure 1A). Use notepad to create a text file with the suffix “.bat” – for example in the figure below, we created a text file containing: save: also saves but not to a specified folder. saveAs “C:Documents and SettingsUserDesktopOutput” See below for more argument items to use via command line. save “C:Documents and SettingsUserDesktopOutput” “C:Documents and SettingsUserDesktopPanel_1.1”Īrguments: for this test, I just wanted my outputs to be saved to this folder called output “C:Program FilesFlowJo vX10.8.0FlowJo_Vx10.exe” Here is an example: I created a template file and specified and output folder after the template is ran. The arguments below can be used just like the Mac. Now you can specify where your template is located, where your data is located, and what other arguments you would like to include in the command. “C:Program FilesFlowJo Vx10.8.0FlowJo_V10.exe” (quotes are very important in the cmd line for XP) Should look like this when finished: using the tab key filled in most of this for me. Then Flo and hit the tab key till you get to the exe file inside the FlowJo program file. Then Flo and hit the tab key to you get the FlowJo program you are using. So to locate XP’s program files and FJ, type in Command LineĬ:Pro and hit the tab key till Program Files is automatically entered. It’s best to use the tab command to find the right file structure with this OS system. At root folder level and the name of the. You will want to open your Programs Folder and make note of the exact FlowJo name. How you invoke FlowJo depends on the operating system. See below for an example.Ĭommand line FlowJo is invoked by referencing an installed version of FlowJo. Note: You must use quotes to reference any file directories that have spaces in them. If it is a workspace, it is stored in the same folder as the template. – Imports the specified folder of external CLR files. Output files may be redirected to a specific folder. – Performs automated exporting of FCS, CSV, or CLR files. – Performs automated batching of layouts and tables. – Loads the data into the workspace, assigning samples to the appropriate groups, performing compensation, gating, and statistic calculations as needed. ![]() If it is an ACS file, the most recent embedded workspace is used. – Opens the specified template (WSPT), workspace (WSP), or ACS file.
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