PEAKS 7 Viewer on Mac OS X Mavericks

I wrote a post in early 2013 here to help users to run PEAKS as a Viewer on Mac OS or Linux. Similar procedure applies to PEAKS 7 as well. Many thanks to user ceinwyn that brought the issue to me that PEAKS DB search results cannot be opened.

I spent some spare time looking into this issue and luckily found a workaround. Just want to re-state my disclaimer here.

Disclaimer: PEAKS does not officially support any OS other than Windows as of the time I am writing the post. The software may not be fully functional. Activating the software on OS X or Linux will consume the license, which means the same license can not be used again. I strongly recommend only following the steps to configure PEAKS Viewer (the unlicensed Studio) on OS X or Linux for PEAKS result sharing and presentation purposes.

Basically what happened here is that PEAKS 7 has some sizing issue with the Auqa look and feel from Apple Mac OS X. The workaround is to change the look and feel to a cross-platform one that Apple also support. To make things easier, I have put a modified version of the jar file here. And here are the steps:

1. Check the version of PEAKS. Go to Help -> About PEAKS. In the dialog, you should see the build number, e.g. build 20131119. This build number must match the number in the downloaded jar file in the above link.
2. Close PEAKS.
3. Download the jar file and replace the peaksstudio.jar in the PEAKS directory with this one.
4. Start PEAKS and now the PEAKS DB search results can be opened. 

Enjoy PEAKS and happy sharing!

A few quick issues of running PEAKS on OS X and Linux

I have played PEAKS as a viewer on a Mac OS X for a while and do notice some minor issues. That's expected as PEAKS on OS X is not officially supported!

No instrument raw file loading ability. This could probably never be fixed unless the instrument vendors port their libraries to OS X. So in short, PEAKS can only read text formats (mgf, mzxml, mzml, pkl, dta, etc) and of course PEAKS projects on OS X.

Images on the summary view is broken. This seems to be a coding issue related to the path (file path on Windows and OS X are different). I do manage to get a workaround though. On the summary view, click "Notes" button on the top of the view, a text editor will show up. Type in the following and click "OK".

<a href="">go</a>

A "go" link will be displayed in the "Notes" section of the summary view. Click on the link, the summary view will be correctly displayed in your default web browser.

Vertical tabs are too small and the text on them are not visible. Well, not sure how to workaround this. But when you mouse over the tabs, the tooltips do work.

I will keep playing PEAKS on OS X when I have chance. Please comment if you find other interesting issues :D

How to run PEAKS Studio/Viewer on Mac OS X or Linux?

Occasionally, we are asked by users whether PEAKS can run on Mac OS X or Linux. PEAKS is written in Java, theoretically it should work. This post will show the steps you need to do to make PEAKS run a Mac OS X. The steps needed should be very similar to make PEAKS work on Linux.

Disclaimer: PEAKS does not officially support any OS other than Windows as of the time I am writing the post. The software may not be fully functional. Activating the software on OS X or Linux will consume the license, which means the same license can not be used again. I strongly recommend only following the steps to configure PEAKS Viewer (the unlicensed Studio) on OS X or Linux for PEAKS result sharing and presentation purposes.

Before you start

PEAKS is a Java program. So before porting PEAKS to Mac, we will make sure that Java is installed. Open a terminal window and type in the command:

java -version

If Java is installed, the version information will be displayed. In OS X Mountain Lion, if Java is not installed, this command will also trigger a window for Java installation.

Get the files

Since PEAKS only have the installer for Windows, you will need a Windows computer to install PEAKS and copy the installed files over to Mac.

To proceed, download PEAKS from the website on a Windows PC. Run the installer, follow the on screen instructions to complete the installation. By default, PEAKS 6 will be installed on C:\PeaksStudio6 directory. Copy the directory to a USB drive and copy it to Mac OS X, e.g. /Users/userx/PeaksStudio6.

Configure PEAKS on OS X

Open a Terminal window and change the directory to the PEAKS directory, for example, /Users/userx/PeaksStudio6, by typing the command:

cd /Users/userx/PeaksStudio6

We need to replace the Windows version JRE with the one installed in OS X:

rm -r -f jre
mkdir jre
cd jre
mkdir bin
cd bin
ln -s /usr/bin/java java.exe
cd /Users/userx/PeaksStudio6

We want to make sure PEAKS starts in one JVM (type the following on one line with a white space after ".jar"):

jre/bin/java.exe -cp peaksstudio.jar com.bsi.tools.computenodenumber.PerformanceConfigDialog

In the performance configuration dialog, select "Manually configure PEAKS performance" option and make sure that the "Start Client Separately" and "Start Compute Node Separately" checkboxes are unchecked. Click "Apply" and close the dialog.

Use a text editor, e.g. vim, to create the start up script peaks.sh:

#!/bin/sh
jre/bin/java.exe -Xmx12000m -splash:splash.png -jar peaksstudio.jar

The number 12000 means that PEAKS can use up to 12GB of RAM. You can change this value based on your computer configuration, but a higher amount is always preferred.

We need to make the script executable:

chmod u+x peaks.sh

Now you can start PEAKS by simply run the script:

./peaks.sh

There are one more thing to do. When PEAKS is opened, go to Preferences. In the "General" section, change the default project folder to a correct directory in OS X.

Now you can view your PEAKS results on a Mac!