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-1-4

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


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