Installing Catalyst on Leopard

I’ve been working with the <a href=””>Catalyst Web Framework</a> most of the summer. I just did a clean install of my system with Leopard. It’s good to flush out the pipes now and again as I’m a chronic shareware user and abuser. In the past, I’ve installed Catalyst by:


 $perl -MCPAN -e ‘install Task::Catalyst’


 $perl -MCPAN -e ‘install Catalyst::Devel’


This works well if you have a mature system and lots of modules already installed. This go around, I thought I’d try out Matt Trout’s <a href=””>Perl installation script</a>. Note that you should already have suitable CPAN configuration in place. Then:


 sudo perl cat-install


The documentation suggests stepping out for a cup of tea. Might I suggest instead coffee. And…it seems to have worked!

New genetic map almost complete

I’m almost done putting the finishing touches on a new Genetic Map display. Intended as a drop-in replacement for the Acedb GMap, the new Genetic Map leverages the GBrowse infrastructure providing a familiar user interface as that for browsing the genome.

I still need to fix a few small things (what in the hell is a centi-centi-Morgan?) 🙂 RD also asked if it might be possible to display mapping data. I think some small modifications of my code that I use for calculating confidence intervals should be sufficient for generating spans for both 2- and 3- factor crosses. The display might get a little complicated displaying separate spans for each experiment – it might be better to aggregate like-experiments together?

Migrating from WordPress to Movable Type

Okay, I know I’m cutting against the grain here but I’m going to migrate back to Movable Type after dabbling with WordPress for a few months. Yes, the installation of WordPress is easier. Yes it’s nice not to have to rebuild pages all the time. The WordPress skins are good but I don’t really have an overwhelming urge to change the look-and-feel of my site every week (heh – or every 5 years).

So why I am returning to Movable Type? The principle reason is entry, comment, and category management. I find these tasks to be incredibly tedious with WordPress. That doesn’t mean that the interface isn’t showing promise. WordPress has some very attractive and innovative features.

Still, I find Movable Type to be far simpler in terms of editing, layout, includes, etc. I vastly prefer the module include system of Movable Type over the php includes of WordPress. And as a Perl programmer familiar with the Template Toolkit System, Movable Types templating system makes much more intuitive sense to me than the egregious PHP functions of WordPress. Personally, I hate PHP. It’s just pure nastiness.

And I have to admit that I find touches like the “Howdy, [user]” to just be needlessly tacky and unprofessional. It’s like inserting expletives in preliminary draft of a manuscript and then forgetting to remove them.

The rebuilding of pages and includes can become incredibly irritating with Movable Type. To minimize this, I do all of my prototyping offline and build a single static design. From there, I can easily break it out into modules and templates as necessary. released to SourceForge

I’ve made a huge number of changes under the hood to make the update process simpler and more stable. A number of things precipitated these changes, including the rapidly expanding size of the database, increasing number of denormalized support databases, the need to run the site in a load balancing situation — and most importantly, the looming addition of 3 new species sometime this year.

I’ve refactored the old Bio::GMOD modules into its own namespace — Bio::WormBase — in part to avoid possible future namespace conflicts as well as too allow a degree of flexibility not present in the old modules.

– Resumable downloads (no longer limited to the Net::FTP/Perl 2GB limit of some architectures).
– purging of old releases
– versioning of all mysql databases, etc, etc, etc
– consolidation and versioning of blast, blat, and epcr databases

To do:
– Service monitoring and restarting as necessary (underway)

You can check out these new modules from sourceforge. I would encourage all of you to become sourceforge developers if you aren’t already so that we can work together to make the mirroring process as streamlined as possible. Please contact me so that I can add you to the list of developers. The project name is bio-wormbase, and the first module is I plan on adding a bunch of other things, such as data mining examples, adminstrative scripts, etc.

Thanks for all your help!


The following documentation is copy-pasted from our Wiki where it is a little easier to read

Fetching the new modules:
Anonymous access:
cvs login
cvs -z3 co -P

Developer access:
export CVS_RSH=ssh
cvs -z3 co -P