GATK Queue and options

[kasthuri]

I did a 'svn update', 'ant clean' and 'ant queue' to install GATK's Queue and I get the message 'BUILD SUCCESSFUL'. However, I don't see any required arguments given in

http://www.broadinstitute.org/gsa/wiki/index.php/Data_Processing_Pipeline

when I invoke >> java -jar dist/Queue.jar --help

Am I missing anything here?

[lletourn]

I don't have an exact answer for you, but I can tell you that you can download a precomplied version from here:
ftp://ftp.broadinstitute.org/pub/gsa...latest.tar.bz2

And when you run
java -jar Queue-1.0.4052/Queue.jar --help

you have the parameters. And when you check the changeset number in svn it's 4052 for queue so I guess it's up to date.

I gave up on queue personnally and rolled out my own solution for the realignment process because I found the scala script too complicated to maintain.

I'm probably just lazy, or I trust my perl, bash talent more than my scala talent :-)

[kasthuri]

Actually, the arguments required a missing parameter which is

-Djava.io.tmpdir=/tmp/queue

They now have a corrected wiki. Thanks for looking into the issue. I still have issues in filtering.