Question: Hints For Integrating The Integrative Genomics Viewer (Igv) In Other Java Based Software?
0
gravatar for Samuel Lampa
8.0 years ago by
Samuel Lampa1.2k
Stockholm
Samuel Lampa1.2k wrote:

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.

java igv • 3.4k views
ADD COMMENTlink modified 8.0 years ago by Jim Robinson250 • written 8.0 years ago by Samuel Lampa1.2k
6
gravatar for Jim Robinson
8.0 years ago by
Jim Robinson250
United States
Jim Robinson250 wrote:

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

ADD COMMENTlink written 8.0 years ago by Jim Robinson250

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).

ADD REPLYlink written 8.0 years ago by Samuel Lampa1.2k

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.

ADD REPLYlink written 8.0 years ago by Jim Robinson250

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

ADD REPLYlink written 8.0 years ago by Samuel Lampa1.2k

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.

ADD REPLYlink written 8.0 years ago by Jim Robinson250

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

ADD REPLYlink written 8.0 years ago by Samuel Lampa1.2k
2
gravatar for Pierre Lindenbaum
8.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum117k wrote:

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"

ADD COMMENTlink written 8.0 years ago by Pierre Lindenbaum117k

That is very useful hints, Thanks!

ADD REPLYlink written 8.0 years ago by Samuel Lampa1.2k
1
gravatar for Malcolm.Cook
8.0 years ago by
Malcolm.Cook1.0k
kansas, usa
Malcolm.Cook1.0k wrote:

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

ADD COMMENTlink written 8.0 years ago by Malcolm.Cook1.0k
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