Java

Solution for "Could not create the Java Virtual Machine"

The problem: we wanted to give more memory to Blast2GO running on Windows 7 x64, but we kept getting the error *beep* "Could not create the Java Virtual Machine".

Looking at the makeJnlp.php file that the Blast2GO website gives you, I noticed the max-heap-size line:

<jnlp spec="1.0+" codebase="http://bioinfo.cipf.es/blast2go/webstart" href="http://bioinfo.cipf.es/blast2go/webstart/makeJnlp.php?mem=2048">
<information>
<title>Blast2GO 2048M</title>
<vendor>CIPF - UPV - IVIA</vendor>
<homepage href="http://www.blast2go.org"/>
<description>Blast2GO 2048M</description>
<description kind="short">Blast2GO 2048M</description>
<icon href="splash.gif"/>
<offline-allowed/>
</information>
<security>
<all-permissions/>
</security>
<resources>
<j2se version="1.5+" initial-heap-size="64m" max-heap-size="2048M"/>
...

When I removed the max-heap-size assignment the JNLP file started just fine with Java Web Start (javaws.exe). Conclusion: somehow the machine could not actually allocate the amount of heap space we were asking for.

Sure enough, further investigation showed that the 32-bit version of Java had been installed instead of the 64-bit version.

After installing the 64-bit version and running the JNLP file with 64-bit javaws.exe, everything was fine.

Blast2GO BLAST results not opening in Mac web browser

If you use Blast2GO on Mac OS X 10.5 Leopard (and haven't been derailed completely by Apple moving Java Web Start around), you might have run into the issue of not being able to view BLAST results in a web browser. Blast2GO even helpfully opens a window for you to choose which browser you want to use, but no matter what you select, nothing happens. Except the following gets written to the Application Messages pane:

Error with choosen Browser! /Applications/Firefox.app: cannot execute

The solution is to tell Blast2GO which browser you want to use. You do that by specifying a path in the blast2go.properties file. You can find the file at /Users/yourusername/blast2go/blast2go.properties.

When you open the file in your text editor* you'll see a property entry under User Pathes (sic) called BlastBrowser.Explorer. You may be tempted to put /Applications/Firefox.app here or even, if you're clever, /Applications/Firefox.app/Contents/MacOS/firefox. But don't do that. Firefox will just complain at you about more than one instance running at a time. Rather, use /usr/bin/open and it will automatically launch the appropriate browser.

// User Pathes
MainGui.Workspace=/Volumes/Data/blast2go_datafile.dat
MainGui.Favorites=/Volumes/Data/blast2go_datafile.dat,
BlastBrowser.Explorer=/usr/bin/open

I ensured that Firefox was the default application to open .fcgi files by creating a text file called foo.fcgi and then selecting Get Info. Probably unnecessary because /usr/bin/open opens URLs in the default browser anyway.

*I used TextWrangler -- if you're still opening files in TextEdit do yourself a favor and download TextWrangler, then make it the default text editor.

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