Thanks very much, sir. 

Is there anything else I need to do specially for the setting up?

Best,

Anthonel



From:   "Fields, Christopher J" <cjfie...@illinois.edu>
To:     "yg...@cpdr.org" <yg...@cpdr.org>
Cc:     "<galaxy-dev@lists.bx.psu.edu>" <galaxy-dev@lists.bx.psu.edu>
Date:   12/13/2012 10:59 AM
Subject:        Re: [galaxy-dev] Questions about Install GATK on local 
instance



Older versions of GATK can be grabbed from Github:

https://github.com/broadgsa/gatk/tags

Not sure if they have an official 'older version' download site.

chris

On Dec 13, 2012, at 9:51 AM, yg...@cpdr.org wrote:

> 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´╝Ü 
> 
> ##### 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 ___________________________________________________________
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