Perl

Running the Generic Genome Browser under PSGI/Plack

September 11, 2011

Here’s a simple approach for installing and running a local instance of GBrowse, leveraging the PSGI/Plack webserver web application stack. You don’t need root access, you don’t need Apache, and you don’t need to request any firewall exceptions (for now). Background Both the current implementation and installer of GBrowse are loosely tied to Apache. By [...]

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Using DropBox for automatic Perl library synchronization

November 28, 2009

Working efficiently across multiple machines just got a whole lot simpler. Working on multiple machines with varied architectures can be a pain. It’s never obvious where the most recent version of something is. Merging changes is tedious and error-prone. Building software over and over is a waste of time. I’ve heard of some gluttons that [...]

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Managing multiple Perl module directories

July 27, 2009

If you develop in Perl or act as a system administrator, you have undoubtedly come up against the hassle of managing local collections of Perl modules. I’ve tried everything in the past. I’ve built modules by hand specifying Makefile.PL prefix paths. I’ve flattened architecture specific directories. I’ve lived through the introduction of Module::Build and the [...]

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Implementing a simple web-log based recommender system

July 25, 2008

I’ve now implemented such a system as an extension to Catalyst, the open source Perl web framework. The system isn’t yet ready for general distribution, but I’d like to share my approach. First, I’ve gathered ten years of web access logs from WormBase, a generic model organism database where I work as the project manager. [...]

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Bizarro Perl problem

June 14, 2008

I just came across a fairly strange Perl issue: Consider: protein => { title => ‘%s release [%s]‘, qq{formatdb_cmd => ‘-p T -t ‘%s’ -i %s’}, filename => ‘protein.fa’, }, Yes, there’s a typo, with the qq enclosing an entire hash entry. This doesn’t raise an error, but obviously obscures the hash entry!

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Installing Catalyst on Leopard

November 3, 2007

I’ve been working with the <a href=”http://www.catalystframework.org/”>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’ [...]

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