Bioinformatics

Installing BioPerl on Mac OS 10.6 Snow Leopard in 6 Easy Steps

The strategy I used to install BioPerl was as follows:

1. Use MacPorts to install Perl.
2. Use CPAN to install BioPerl.

Here are the nitty gritty details. You need a live internet connection, as both MacPorts and CPAN expect to be able to download packages.

Step One: XCode Tools

Before MacPorts can be installed, XCode Tools needs to be installed. This is free from Apple and can be installed from the original OS X 10.6 DVD or downloaded from Apple's developer site.

Thanks for testing, OWC

Other World Computing tested whether the 2009 Mac Pro could go to 64GB (no affiliation; I'm just a happy customer). I can now confirm this.

I only wish it were my machine. :)

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:

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.

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