Question: GATK2 tools installation
gravatar for Marc
3.4 years ago by
United Kingdom
Marc30 wrote:

Hi all, 

Why the installation of gatk2 stuck at the status of cloning? I've done this before and it worked fine. 

Another question is that the GATK2_PATH(type: set_environment), do I need do any configuration or anything at all about this? Because the GATK2 tools didn't work before due to unable to access GenomeAnalysis.jar, when I was able to install them.


gatk local galaxy • 1.2k views
ADD COMMENTlink written 3.4 years ago by Marc30

Did you recently update your Galaxy instance? I just did (now running v15.05) and I'm also running into the same issue with installing the gatk2 repository. We had it previously, but I would have to confirm whether it was also installed using the same method or had a similar issue. 

ADD REPLYlink written 3.4 years ago by bgrande40


Yeah I did Install the latest one. So how should I fix it? Looking forward to your reply. Also, do you happen to know the answer to my other question? And when you install gatk2 from the toolshed, other than click install, is there anything else that needs to be configured?

Many thanks

ADD REPLYlink written 3.4 years ago by Marc30

Unfortunately, I'm basically in the same boat as you. Based on your answer, it seems that this issue is specific to the latest version of Galaxy, suggesting an issue with Galaxy and not the gatk2 repository. This is something that should be brought up with the Galaxy team. I'll email them on their developer mailing list. 

To address your second question, this is my first time installing this repository myself. However, based on the documentation, once it's installed properly (which we are unable to do at the moment), you need to download the GATK programs to wherever Galaxy is running. Afterwards, you must edit the gatk2 file (see documentation for where you can find this) such that it points to the GATK installation. This is my understanding, but I can't test it at the moment. 

ADD REPLYlink written 3.4 years ago by bgrande40
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