Todd Harris, PhD

Facilitating scientific discovery at the intersection of genetics, genomics, bioinformatics, big data, cloud computing, and open science.

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profiling memory usage

February 8, 2006 By Todd Harris Leave a Comment

Just came across this interesting mailing list post on profiling memory usage on Linux.

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Filed Under: howto Tagged With: sysadmin

MediaWiki and reverse proxy

February 4, 2006 By Todd Harris 6 Comments

I’ve been trying to ProxyPass from a primary server to a backend (but not firewalled) machine running MediaWiki 1.5.2 with very little luck.

I finally come across the solution. backend.machine.edu is the machine hosting MediaWiki. frontend.machine.edu is the machine acting as a reverse proxy.

1. Proxy machine, httpd.conf


ProxyPass /wiki http://backend.machine.edu/wiki

2. On backend.machine.edu edit DefaultSettings.php

$wgServer = ‘http://frontend.machine.edu’;

This *shouldn’t* be necessary as this variable can also be provided in LocalSettings.php. However, I found the early stages of the request cycle were not correctly resolved to the front end machine.

3. Edit LocalSettings.php

Add the (possibly redundant) $wgServer variable

$wgServer = ‘http://frontend.machine.edu’;

I also found that the absolute image path for the Wiki Logo was not resolving correctly through the proxy. Correct this (if necessary) by setting $wgLogo. This assumes that your backend machine is not behind a firewall.

$wgLogo = “http://backend.machine.edu/images/wikilogo.jpg”;

4. Edit squid.conf on squid.machine.org to exclude wiki content

I might want to revisit this decision in the future. For now, I’d rather not fill our cache with Wiki material, saving that space for the heavier acedb content.

acl wiki url_regex -i wiki
no_cache deny wiki

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Filed Under: howto Tagged With: sysadmin

Future-proofing movable type URLS

February 1, 2006 By Todd Harris Leave a Comment

Here’s a useful tutorial on future proofing the irritating stub-based URLs of movable type (and many blogging systems).

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Filed Under: development Tagged With: blogging

sending email

January 30, 2006 By Todd Harris Leave a Comment

Just came across this interesting tutorial on sending email from shell scripts. Very useful.

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Filed Under: howto Tagged With: shell scripting

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Welcome!
My name is Todd Harris. A geneticist by training, I now work at the intersection of biology and computer science developing tools and systems to organize, visualize, and query large-scale genomic data across a variety of organisms.

I'm driven by the desire to accelerate the pace of scientific discovery and to improve the transparency and reproducibility of the scientific process.

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