Common Installation Issues with FlowJo™ v10.1

Installing FlowJo on a Mac or Windows machine is now very simple and fast. However, there are a few considerations for new users, old hands, or even IT departments responsible for completing this process.

For one thing, the “bitness” of your FlowJo installation must match the bitness of your computer. Though many 32-bit applications can be installed on 64-bit machines, FlowJo prevents this operation in order to assure our customers receive the most performant experience possible for their system.

In some rare cases, a specific exception needs to be made to an institution's security protocols to allow FlowJo’s installer to run unobstructed. This can be due to the uncertified nature of the application on Windows environments, or related to the older edition of Java that FlowJo v10 requires. In these cases, it is the responsibility of personnel who control a machine’s security (typically an IT department) to investigate this exception and make the necessary changes there.

Some legacy FlowJo users have a hard time letting go of their old FlowJo applications! Wanting to hold on to the older versions of a software we’ve come to love is understandable, and not as uncommon as one might think. Rest assured that there is nothing preventing you from hanging onto your copy of FlowJo v10.0.7r2 (for example). In this case, you should make sure that your latest FlowJo install is placed in its own uniquely-named folder within the Program Files folder.

Note: The following procedures are for Windows operating systems only.

To perform a fresh install (if you are not overly attached to your legacy install):

Find and run the ‘Uninstall FlowJo’ application from the Programs and Features section of their Control Panel. Double-check that the previous install has been completely cleaned out of the Program Files folder before performing the new install.

To keep your legacy install:

Run FlowJo’s installation wizard normally, but enter a new name for the install folder within the appropriate dialog (See Figure 1).

 

Figure 1. FlowJo Installation Wizard, showing the Choose Install Folder dialog.

On Mac OSX, FlowJo requires users to manually downgrade their Java environment to Java SE 1.6. You can find a link to download this version of Java from the minimum requirements section of our Mac downloads page (See Figure 2):

www.flowjo.com/download-for-mac/

 

Figure 2. FlowJo Download for Mac page, showing Java for OSX link.

The Java downgrade is not required for Windows machines because the Java SE 1.6 package is included in the FlowJo v10 installer for Windows.

Regarding site-wide installations (especially for customers of the IT variety), you can now perform a silent install of FlowJo! The silent installation process allows an IT wizard to install programs, usually for many machines across a lab, through a fancy command-line script maneuver. The command script to run a silent install for FlowJo’s 64-bit Windows installer looks like this:

FlowJo-Win64-10.1r7 -i silent

This process is not recommended for those without command-line skills (or those with a heart condition!)

For more information regarding proper install procedure, check out the documentation available here:

docs.flowjo.com/d2/installation/

If you still have specific questions regarding your install of FlowJo always feel free to email: techsupport@flowjo.com

Comments

[Waldemar Racki]

Hi,

We have recently upgraded FlowJo as prompted by program itself to the current version 10.2 Engine v3.05470.
We have what looks like compatibility problem - the newer version does not correctly recognize the templates created with previous FlowJo. It can open the template, load samples, but the analysis is not correct. Gates created in the template do not show correctly on the corresponding plots. Also, it doesn't properly attribute events for statistics - counting all events as zero.
Thank you in advance,
Waldi

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