Hints For Integrating The Integrative Genomics Viewer (Igv) In Other Java Based Software?

Question

[Samuel Lampa]

I'm looking for integrating the Integrative Genomics Viewer (IGV) from Broad Institute, into the Java/Eclipse based bioinformatics platform Bioclipse.

I thought someone might have integrated IGV to other software before, and so could provide some hints about the best approach, any good guides / reference material to read, etc?

EDIT: Hints about integrating also the GUI components into other Java software is the most interesting, since we want IGV to be able to be started completely inside Bioclipse.

Answer 1

[Jim Robinson]

Hi,

This is Jim Robinson, developer of IGV. I'm interested in helping (i.e. answering) questions on this subject, but don't have much time to work on it. However, don't consider yourself limited by the current options, if there are changes I could make to make IGV more "pluggable" I'm open to entertaining them, particularly if you or others could help with the programming.

I don't normally follow this forum, so if you want to follow up its best to email igv-help (at) broadinstitute.org

Cheers

Jim

[Samuel Lampa]

Thanks Jim, that sounds marvelous! I'll try to summarize my initial questions + details on what we try to do in a mail to igv-help then! (I guess we can bring back the hints we figure out here later).

[Jim Robinson]

Sure, we can carry on the conversation here if that makes sense so others can benefit, just ping me at igv-help if I don't respond.

[Samuel Lampa]

Ok, sound fine, though for longer / more detailed questinos it seems mail (+ summarizing any general hints here) might be better. I'll first try to see if I can get IGV running from source code, in Eclipse, and will probably have more questions after that! Cheers / Samuel

[Jim Robinson]

I suggest using the 2.0 source code, not yet released but will be soon. We've setup a google code repository for that http://code.google.com/p/igv/ If you would prefer the code in a zip archive let me know. Setup should be straightforward, all the jars are in "lib" and the main routine is in org.broad.igv.ui.Main.

[Samuel Lampa]

Excellent, thanks! (svn checkout will do fine!)

Answer 2

[Pierre Lindenbaum]

My two cents: I know (from a previous Q&A on Biostar?) that you can start a Process for IGV with a few arguments on the command-line: see http://code.google.com/p/igv/source/browse/trunk/src/org/broad/igv/ui/IGVMainFrame.java

CmdLineParser.Option propertyFileOption = parser.addStringOption('p', "preferences");
CmdLineParser.Option batchFileOption = parser.addStringOption('b', "batch");
CmdLineParser.Option genomeOption = parser.addStringOption('g', "genome");

See also "Running IGV with a batch file"

[Samuel Lampa]

That is very useful hints, Thanks!

Answer 3

[Malcolm.Cook]

Controlling IGV through a Port is possible, which allowed me to Control IGV from Excel or other Macintosh/Windows Application using Applescript/VBA