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Old 12-22-2015, 01:47 PM   #1
jinxiama
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Registered: Dec 2015
Posts: 2

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Unhappy GATK installation


Hi all,
I am new to linux, and trying to install GATK on my Mac Pro. Does anybody can give me any suggestions?
Thanks.
 
Old 12-22-2015, 02:15 PM   #2
TB0ne
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Registered: Jul 2003
Location: Birmingham, Alabama
Distribution: SuSE, RedHat, Slack,CentOS
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Quote:
Originally Posted by jinxiama View Post
Hi all,
I am new to linux, and trying to install GATK on my Mac Pro. Does anybody can give me any suggestions? Thanks.
Read the "Question Guidelines" link in my posting signature, please.

First, Mac's do NOT run Linux by default, unless you did a manual installation...did you? If so, then you need to tell us what version/distro you're running, and what you have done/tried on your own.

Secondly, we will suggest that you go and look up the website and read the documentation.
https://www.broadinstitute.org/gatk/download/

We are always happy to help, but we can't (and WON'T) read documentation for you. Give us a specific problem you're having, and we can help.
 
Old 12-22-2015, 02:36 PM   #3
jinxiama
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Registered: Dec 2015
Posts: 2

Original Poster
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Wink

Hi TB0ne,
Thank you for your reply, and sorry for my unclear question. I downloaded GATK (GenomeAnalysisTK-3.5) and unzipped as GenomeAnalysisTK.jar. I have problems with installing it. I could not install it by double clicking it. while when I use Terminal, it told me that "permission denied". Does that mean I have to get access to "root"? My system information: OS X El Capitan 10.11.2 and I also find one article says "OS X El Capitan kills root". I am not sure what does that mean. My Java version is 1.8. Could you help me with this ?Thanks a lot!
 
Old 12-22-2015, 02:54 PM   #4
TB0ne
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Registered: Jul 2003
Location: Birmingham, Alabama
Distribution: SuSE, RedHat, Slack,CentOS
Posts: 21,935

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Quote:
Originally Posted by jinxiama View Post
Hi TB0ne,
Thank you for your reply, and sorry for my unclear question. I downloaded GATK (GenomeAnalysisTK-3.5) and unzipped as GenomeAnalysisTK.jar. I have problems with installing it. I could not install it by double clicking it. while when I use Terminal, it told me that "permission denied". Does that mean I have to get access to "root"? My system information: OS X El Capitan 10.11.2 and I also find one article says "OS X El Capitan kills root". I am not sure what does that mean. My Java version is 1.8. Could you help me with this ?Thanks a lot!
AGAIN:
  • Mac's DO NOT RUN LINUX by default. DID YOU INSTALL IT? If so, what version/distro??
  • Did you read/understand the installation instructions on their website?
  • That "permission denied" message MAY mean you need root, but we don't know (because you haven't TOLD US), what operating system you're running.
Provide details and we might be able to help.
 
Old 01-15-2016, 10:24 PM   #5
vdauwera
LQ Newbie
 
Registered: Jan 2016
Posts: 1

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There is no installation necessary for GATK, you just have to have the correct version of Java (1.7 for GATK 3.5). Then you simply call the GATK jar file from command line (there is no GUI, no clicking involved anywhere). There are plenty of example command lines in the GATK documentation.

(I am the GATK support lead)
 
  


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