AutoGate installation and launching is designed to seamlessly work on your computer. In most cases, it has been proven to work that way.However, there have been isolated instances where installing/launching AutoGate have been an average experience.As we have limited control over 3rd party softwares that are installed as part of the pre-requisites and the complexity around user environment in some cases, it is hard to handle all scenarios. Hence, the below article to help you be aware of the most common messages and the ways to address it.  We believe the proposed responses here will most likely enable you to progress further and successfully launch AutoGate.

If at any time during the launch process you experience any new messages or alerts that is not captured here, please reach out to our support and we will be glad to assist you. Sharing this information with us, will also help other users who may encounter similar experience.

 

1. After you upgrade MAC OS, you will get an alert To open AutoGate.app you need to install the legacy Java SE 6 runtime

Click More info. This will take you to the relevant Java SE6 page. Click Download. When it completes, double-click JavaForOSX.pkg. The installation window will display. Follow the directions and you will have what you need to run AutoGate.

LaunchingAutoGate

 

2. On trying to launch AutoGate on Mac, there is a message that its from an Unidentified developer.

Unidentified developer

This is a common message, if Mac can't check whether AutoGate has been modifieid since it was released. This doesn't mean that's something wrong with AutoGate. Click Open and you will be fine

If the above message does not have an 'Open' option, then follow the below steps.

i). In the Finder window, locate AutoGate.app

ii). Press the Control key, then click the app icon, then choose Open from the shortcut menu.

iii). Click Open.

 

3. On trying to launch AutoGate on Mac, there is a message that AutoGate is an application downloaded from the Internet.

Again, this is a common message from Mac. Click Open to continue

fromInternet

 

4. On trying to launch AutoGate on Mac, there is a message that its damaged and can't be opened

damaged

i). Open Terminal

ii). Type sudo bash. Enter your password

iii). Type xattr -cr /Applications/AutoGate.app

damaged terminal

iv). Close Terminal

v). Open AutoGate now

Note: If you are on older version of Mac OS, then instead of the above steps, Open Security & Privacy under System Preferences and choose Anywhere option, as below.

 downloadanywhere

 

5. AutoGate crashes on trying to launch on Mac.

This is due to Java 1.6 version on your Mac. Install the Patch from Apple site here

6. Even after fixing the AutoGate.app is damaged error, AutoGate fails to launch on the new MAC OS Sierra. Error being AutoGate quit unexpectedly.

AutoGate Quit

This is due to incompativle Java 1.6 version

i) Using Finder, go to /Library/Java/JavaVirtualMachines

ii) Select the java 1.6 and delete

Java Delete

iii) Launch AutoGate. It will alert to install the legacy Java SE6 runtime. Click on More info link and follow the instructions. Once installed, launch AutoGate again

7. On trying to launch AutoGate on Mac, there is a message that the installed Matlab Runtime is not compatible with the application. 

Matlab incompatibility error

In almost 99% of the scenarios, AutoGate installer will install the pre-requisites (Java and Matlab Runtime) on users computer without any problem. But in few scenarios, it may prove difficult to install these 3rd party soffwares, due to number of factors( eg, users' computer configuration, computer capacity, conflicting softwares, antivirus, network policies,..). In those scenarios, it is recommedned that users install Matlab Runtime directly from Mathworks site - https://www.mathworks.com/products/compiler/mcr.html

Once Matlab Runtime is installed, proceed with AutoGate launch.

 

8. On trying to launch AutoGate on Mac, there is a unclear message Cannot locate a valid install area..

valid install area

This is related to Matlab version not available or installed on the user computer.

In almost 99% of the scenarios, AutoGate installer will install the pre-requisites (Java and Matlab Runtime) on users computer without any problem. But in few scenarios, it may prove difficult to install these 3rd party soffwares, due to number of factors( eg, users' computer configuration, computer capacity, conflicting softwares, antivirus, network policies,..). In those scenarios, it is recommedned that users install Matlab Runtime directly from Mathworks site - https://www.mathworks.com/products/compiler/mcr.html

Once Matlab Runtime is installed, proceed with AutoGate launch.

 

9. On trying to launch AutoGate on Mac, there is a message Test Matlab2016b or AutoGate2016b cannot be opened.

TestMatlab

AutoGate2016

This is related to Matlab Runtime not properly installed or available in the expected location.

In almost 99% of the scenarios, AutoGate installer will install the pre-requisites (Java and Matlab Runtime) on users computer without any problem. But in few scenarios, it may prove difficult to install these 3rd party soffwares, due to number of factors( eg, users' computer configuration, computer capacity, conflicting softwares, antivirus, network policies,..). In those scenarios, it is recommedned that users install Matlab Runtime directly from Mathworks site - https://www.mathworks.com/products/compiler/mcr.html

Once Matlab Runtime is installed, proceed with AutoGate launch.

 

10. Computer tells that AutoGate is "damaged" or "dangerous?

Click Cancel or Discard and carry on.

 

11. On trying to launch AutoGate, there is a prompt about Incoming connections.

Yes, it is safe to allow incoming connections from Cytogenie.org

 

Locate the files that hold your earlier experiments, whether from your flow cytometry insturment or analysis software such as DiVa, CellQuest Pro, or FlowJo. You should put them into a single folder where AutoGate can easily find them.

AutoGate icon

The installation program has put your AutoGate icon (shown above) on your desktop. Double-click it. Your first launch will take a few minutes while the program loads the files it needs. You may also experience minor delays whenever the program automatically downloads our periodic updates. Whether you last used AutoGate the night before or a year ago, it will scan your program files to make sure you have our latest and greatest.

As AutoGate launches, a screen will display our simple license agreement.

license agreement

To use AutoGate, click I agree.

 

As mentioned in the pre-requisites for AutoGate, it requires Matlab to work. The production version of AutoGate uses Matlab version 2017a. To take advantages of recent update of Matlab, we are releasing an early adopter version (EAV) of AutoGate with Matlab R2019a. If you would like to participate in this EAV, below are the details. Once we have proven AutoGate's compatibility with Matlab R2019a, we will release this to wider community.

 

For Mac Users

1. Download Matlab R2019a runtime from https://www.mathworks.com/products/compiler/matlab-runtime.html.

This is a once off install and doens't have to be repeated when there's a newer version of AutoGate.

1) It takes ~15 mins to complete the download (depending on your computer configuration and network speed)

 2019aMCR Downloa

 

2) Go to Downloads folder and extract the zip

 

3) Open the MATLAB_Runtime_R2019a_Update_5_maci64.dmg file

2019aMCR Unzipped

 

4) Open the Install file

2019aMCR Install

 

5) As it's downloaded from a trusted site, click Open

2019aMCR Open

 

6) Provide your computer admin credentails when prompted

2019aMCR Java pwd

 

7) It takes ~5 mins for the Matlab Install Wizard to show up. No changes / action required here or in any of the installation steps.

2019aMCR Install append

 

8) Click on the Next button in all the screens to complete the installation.

2019aMCR Install complete

 

2. Download AutoGate2019a.app from http://cgworkspace.cytogenie.org/GetDown2/domains/FACS/AutoGate2019a.tar

 

1) It prompts to Open with or Save File. Click OK

AG2019a Download

 

2) Go to Downloads folder and open AutoGate2019a.app. Though AutoGate2019a.app is from a trusted source, Mac computer displays this warning message. Click Cancel

AG2019a App Cancel

 

3) Again open AutoGate2019a.app from the downloads folder. This time, click Open

AG2019a Open

 

4) AutoGate2019a will launch.

When there's a new version of AutoGate available, we will notify you on the steps to get the updates.

As mentioned in the pre-requisites for AutoGate, it requires Matlab to work. The production version of AutoGate uses Matlab version 2020a Runtime. When you download AutoGate from http://www.cytogenie.org, it will install Matlab R2020a for you. If you prefer to install on your own, below are the steps to install and then launch AutoGate.

 

For Mac Users

1. Download Matlab R2020a runtime from https://www.mathworks.com/products/compiler/matlab-runtime.html.

2020aMCR Runtime

This is a once off install and doens't have to be repeated when there's a newer version of AutoGate.

1) It takes ~15 mins to complete the download (depending on your computer configuration and network speed)

2020MCR download

 

2) Go to Downloads folder and extract the zip

 

3) Open the MATLAB_Runtime_R2012a_Update_2_maci64.dmg file

2020aMCR unzipped

 

4) Open the Install file

2020aMCR Install

 

5) As it's downloaded from a trusted site, click Open

2020aMCR Alert

 

6) Provide your computer admin credentails when prompted

2020aMCR adminpwd

 

7) It takes ~5 mins for the Matlab Install Wizard to show up. No changes / action required here or in any of the installation steps.

 2020aMCR Install NoChanges

 

8) Click on the Next button in all the screens to complete the installation.

2020aMCR Install complete

 

2. Download AutoGate2020a.app from http://cgworkspace.cytogenie.org/GetDown2/domains/FACS/AutoGate2020a.tar

 

1) Go to Downloads folder and Unzip AutoGate2020a.tar

 

2) Open AutoGate2020a.app

 2020aMCR AG Open 

  

3) Though AutoGate2020a.app is from a trusted source, Mac computer displays this warning message. Click Cancel

2020aMCR AG Alert

 

4) Again open AutoGate2020a.app from the downloads folder. This time, click Open

2020aMCR AG Open AfterAlert

 

5) AutoGate with Matlab 2020a will launch.

2020aMCR AG Launched

When there's a new version of AutoGate available, we will notify you on the steps to get the updates.

 

From version 4.586, AutoGate will work with the latest release of Matlab 2020a.

Existing users - When you launch AutoGate, it will check for availablility for Matlab 2020a. If not available, it will get your consent and do the installation for you. It's a pretty straight forward process and should take no more than 30 mins to complete. It's a once -off installation and not required to repeat.

Below are the steps for Mac users, for reference. If you encounter any issues, please contact  and we will be glad to assist you.


Existing users:

1. Open AutoGate.app

2. AutoGate will check for AutoGate. As this is a critical update, Users are advised not to skip.

1.Checking updates

 

3. AutoGate will then download the updates

1.Checking updates 

 

4. Below alert will be displayed, if Matlab 2020a isn't available. This alert is displayed by Matlab and AutoGate doesn't have control over it. Click OK

4.Cannot locate

 

5. User will now be presented with a choice to swithc to 2020a or continue with 2017a. It's recommended to switch, as support for Matlab 2017a is only for a limited period. 

Click yes, install now to proceed with switching. If you wish to do this the next time, click No.

5.Prompt with choice

 

8. The launcher will get ready to commence the installation

1.cannot locate

 

9. Provide your admin credentials so any Matlab specific changes can be made

1.cannot locate

 

10. Matlab 2020a Runtime install wizard will show up. Click Next

1.cannot locate

 

11. Click Next if you are okay with the default installation location

1.cannot locate

 

12. Click Next

1.cannot locate

 

13. Click Yes to the license agreement

1.cannot locate

 

14. Click Install

1.cannot locate

 

15. Download of Matlab will progress

1.cannot locate

 

16. Once download is completed, click Finish. Note, you can disregard the instructions in this window

1.cannot locate

 

17. Open AutoGate.app again from the Applications folder

18. AutoGate will launche with Matlab 2020a

3.Launched AG

 

From version 4.586, AutoGate will work with the latest release of Matlab 2020a.

Existing users- When you launch AutoGate, it will check for availablility for Matlab 2020a. If not available, it will get your consent and do the installation for you. It's a pretty straight forward process and should take no more than 30 mins to complete. It's a once -off installation and not required to repeat.

Below are the steps for Windows users, for reference. If you encounter any issues, please contact  and we will be glad to assist you.


Existing users:

1. Open AutoGate.exe

 

2. AutoGate will check for AutoGate. As this is a critical update, Users won't have the choice to Skip.

2.Checking 4 update

 

3. AutoGate will then download the updates

3.Downloading Updates 

 

4. Below alert will be displayed, if Matlab 2020a isn't available. This alert is displayed by Matlab and AutoGate doesn't have control over it. Click OK

4.2020a not available

 

5. User will now be presented with a choice to swithc to 2020a or continue with 2017a. It's recommended to switch, as support for Matlab 2017a is only for a limited period. 

Click yes, install now to proceed with switching. If you wish to do this the next time, click No.

5.Alert Choice

 

6. On clicking Yes, install now, the launcher will get ready to commence the installation

 

7. Provide your admin credentials so any Matlab specific changes can be made

8. Matlab 2020a Runtime install wizard will show up. Click Next

6.Matlab Installer

 

11. Click Next and progress through the screens to complete the installation

12. Once download is completed, click Finish. Note, you can disregard the instructions in this window

1.cannot locate

 

17. Open AutoGate.exe again

18. AutoGate will launch with Matlab 2020a

 

Click below for step by step process involved with launching AutoGate using Matlab R2020a.

Mac users, click here

Windows users, click here

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