Hi,
Could anyone give me some
suggestions about that?
Thanks very much.
Anthonel
----- Forwarded by Yixiao
Gong/cpdr/hjf on 12/13/2012 10:50 AM -----
From:
Yixiao Gong/cpdr/hjf
To:
galaxy-dev@lists.bx.psu.edu
Date:
12/12/2012 02:52 PM
Subject:
Questions about
Install GATK on local instance
Hi, all,
I'm installing GATK on galaxy local
instance now and I have some questions may need your help.
I downloaded the GATK2 from GATK website
htt http://www.broadinstitute.org/gatk/download
. the link is http://www.broadinstitute.org/gatk/auth?package=GATK
I knew that on galaxy tool dependencies
page http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
they gave the link for GATK 1.4 version
but I can't figure out how to download and install it, and I noticed that
GATK2 have all 1.x version features, so I installed GATK2.
In the GATK 1.4 link (https://github.com/broadgsa/gatk
) that shown on http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies,
there are multiple folders and files and I got really confused what I need
to download. Even I choose "ZIP" to download a zip file, I counld
not figure out whether it is the program package and don't know how to
install it.
Maybe this is the problem. But based
on my understanding, GATK is just a set of java package, and all we need
to do is put it into /tool-data/shared/jars folder, right? That is how
I did it for GATK2. The GATK2 package include a folder called "resources"
and a file called "GenomeAnalysisTK.jar" . I put them into /tool-data/shared/jars/gatk
folder. I tested the installation following the instruction : http://gatkforums.broadinstitute.org/discussion/1200/how-to-test-your-gatk-installation
And I request a key from broadinstitute
and followed the instruction on http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest
But the galaxy still gave me the error
message as followed£º
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.2-16-g9f648cb):
##### ERROR The invalid arguments or inputs must be corrected before the
GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view
allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and
answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires
a GATK Key file. Please see http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest
for more information and instructions on how to obtain a key.
##### ERROR ------------------------------------------------------------------------------------------
I guess I may made mistakes in some
point:
1. I should not install GATK2 but only
GATK 1.4 so that Galaxy can use it. But I really don't know how to download
and install it. I can't find the correct file.
2. GATK2 works on Galaxy but I did something
wrong on installing it.
Could anyone help me about this? It
will be greatly appreciated.
Thanks.
Anthonel