Thanks very much, sir.
Is there anything else I need to do specially for
the setting up?
Best,
Anthonel
From:
"Fields, Christopher
J" <cjfields@illinois.edu>
To:
"ygong@cpdr.org"
<ygong@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, ygong@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£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 ___________________________________________________________
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