Argo Frequently Asked Questions (FAQ)

How is this page organized?

Somewhat haphazardly. Your best bet might be to control-F (or apple-f) for the terms you are looking for. I've consciously included common synonyms and alternate terms.

When I try to run argo, I get the error "cannot find the main class." What should I do?

It probably means you don't have java 1.5 or higher installed on your computer. You should be able to tell this by going to the command line and typing:

java -version

This should yield something like:

java version "1.5.0_06"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_06-112)
Java HotSpot(TM) Client VM (build 1.5.0_06-64, mixed mode, sharing)

If you do indeed have the correct version of java installed but argo still doesn't run when you click it, it means that your operating system has not been configured to open jar files using java. How to fix this depends on your operating system (links pending); it is normally set up by the java installer. You can also manually run argo or other jars from the command line (or batch file) using the syntax:

java -jar argo.jar

See also how to give argo more memory by running it from the command line.

Can Argo edit features?

Yes. Argo can edit (insert, update, delete) features in GTF2 format. Argo can export features in a variety of other formats.

What track file formats can Argo display?

GFF, Genbank, Genscan, and Blast.

If you have data in another format that you would like to display, you can do one of two things:

  1. convert it to one of the above formats (gff is probably easiest, many analysis programs come with the option to produce gff output)
  2. if you think there is widepread demand to view data in this format, let us know, and we'll consider building in support in a future release.

How do I select the transcript of a single exon transcript?

or

How do I convince Argo to open a really big feature map without running out of memory?

By default, java doesn't allow applications a whole lot of memory. You can increase this at the command line, though.

Try running something like:

java -Xms32m -Xmx384m -jar argo.jar

In the statement above, 32m is the megabytes of memory to start the program with, the 384 is the maximum memory.

How do I select the parent of a single subfeature feature?

Some compound features consist of only a single subfeature. Since the subfeature spans the whole length of the parent, you can't select the parent by clicking on it, it's effectively "behind" the subfeature. To select the parent, click the subfeature and then choose "Select Parent" from the Edit menu. "Select Parent" is also a right click popup menu option.

My question wasn't answered here! How do I get help?

Send us your questions. We're eager to assist you. See the contact information at the bottom of this and every other page on this site.


Last Updated: Sept 18 2006
Contact: Reinhard Engels
argo-support@broad.mit.edu