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

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: 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-i...

And I request a key from broadinstitute and followed the instruction on

http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-...

But the galaxy still gave me the error message as followed：

##### 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-... 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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/

Chris, Anthonel Compiled versions of older GATK releases can also be found via this forum discussion: http://gatkforums.broadinstitute.org/discussion/1563/download-gatk-version-1... This has a link to GATK binaries hosted at: https://www.dropbox.com/sh/1misjysdehceq4h/GnQB948vMl HTH Best wishes, Peter On 13/12/12 15:59, Fields, Christopher J wrote:

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-i...

And I request a key from broadinstitute and followed the instruction on http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-...

But the galaxy still gave me the error message as followed：

##### 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-... 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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/

-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482