Integrated Genome Browser (IGB, pronounced “ig-bee”) is an application built upon the GenoViz SDK and Genometry for visualization and exploration of genomes and corresponding annotations from multiple data sources. IGB is also a client for the DAS (Distributed Annotation System) protocol.
I’m going to see if I can get IGB on my Mac to connect to a local Perl DAS/2 server I’m writing. This section is for Gregg to see my progress (more likely lack thereof) and slap me if I stray too far. –Jhannah 14:30, 7 November 2007 (EST)
Gregg instructions from a Windows client:
In your user home directory (not sure exactly where that is on Mac),
IGB sets up an igb_prefs.xml file. To add more DAS/2 servers to IGB,
add a line like this to the file:
<das2_server name="localhost" url="http://localhost:9092/das2/genome" />
Unfortunately on a Mac this apparently isn’t so straight forward. My preferences are getting stuck here:
/Users/jhannah/Library/Preference/com.affymetrix.igb.plist
And OS/X is whacking the XML in very creative ways, into this key/dict structure:
...
<key>das2/</key>
<dict>
<key>http:%%netaffxdas.affymetrix.com%das2%genome/</key>
<dict>
<key>http:%%netaffxdas.affymetrix.com%das2%genome%H_sapiens/</key>
<dict>
<key>http:%%netaffxdas.affymetrix.com%das2%genome%H_sapiens_Mar_2006/</key>
<dict>
...
So I’m trying to reverse engineer how I can add my localhost as a DAS/2 server.
UPDATE from Gregg: The preferences stored in the *.plist file are serialized Java Preferences nodes, which are different from the preferences kept in the “igb_prefs.xml” file – IGB uses both. If you’ve run IGB there should be an “igb_prefs.xml” file in your home directory, which on OS X is usually /Users/[user_id]/. That’s the file where you need to add the das2_server line.
I’ve hit several apparently out-of-date things in the downloadable IGB_User_Guide.pdf… I’m not sure if Gregg is interested in me submitting documentation errata or not. (e.g.: “Exporting Preference Settings” seems to have disappeared.)
UPDATE from Gregg: Yep the IGB User’s Guide definitely needs an update. I wouldn’t worry about listing all the places the docs don’t agree with the current release – there’s a lot of those. If you encounter any problems with IGB there is a discussion forum set up: https://www.affymetrix.com/community/forums/forum.jspa?forumID=28
Command line:
plutil -convert xml1 -o j com.affymetrix.igb.plist
plutil -convert binary1 -o com.affymetrix.igb.plist j
defaults read com.affymetrix.igb
GUI:
/Developer/Applications/Utilities/Property List Editor.app
(Part of the OS/X Developer Toolkit)