Problem Installing and testing GATK-4.1.7.0
Hi there,
Need help for beginner. I have a problem testing gatk-4.1.7.0. I am new to both Linux system and GATK. I am following (https://gatk.broadinstitute.org/hc/en-us/articles/360041320571--How-to-Install-all-software-packages-required-to-follow-the-GATK-Best-Practices) and was able to install BWA, SAMtools, and Picard and successfully test those. To make long story short, I downloaded gatk-4.1.7.0 (Download release :gatk-4.1.7.0.zip) using (https://github.com/broadinstitute/gatk/releases), uzipped it and placed in Desktop directory. Then, according to the guideline in Getting Started with GATK4 (https://gatk.broadinstitute.org/hc/en-us/articles/360036194592-Getting-started-with-GATK4) section 5 (Install it) I set path for gatk in .bashrc. as given below. The same thing I did for bwa and samtools.
export PATH=$PATH:"/home/arjun/Desktop/gatk-4.1.7.0/gatk"
Assuming that after I set path I can test gatk directly from terminal, I used command
gatk --help
I am getting “Command 'gatk' not found, did you mean:…” and few other lines.
Note. I am using python3 version (Python 3.8.2). Guideline says “You will need Python 2.6 or greater to run the gatk wrapper script”. Also, the java version I am using is “openjdk version 1.8.0_252”. I believe this is java version 1.8 as described in guideline.
Please help me to figure out the problem with installation/testing of gatk. I tried to look previous posts but could not figure out.
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Hi Arjun Upadhaya , I think this is an issue with how you set up your path.
What displays when you run:
echo $0
What about
echo $PATH
Can you confirm the path to the executable? You can navigate to the gatk folder (cd gatk-4.1.7.0) and run ./gatk to execute commands from there while you debug the path issue. I know you did all the work to install the other software required, but running via Docker is also a great way to go.
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Thank you Tiffany for the suggestions and quick response. I tried few things and the problem was solved.
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Good to hear. What worked for you (it may help others)? We updated the docs to include a suggestion with adding an alias to your bash profile that points to the gatk python script.
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Thank you Tiffany. I should have explained previously what I did. Previously, my path to gatk executable in .bashrc was wrong "export PATH=$PATH:"/home/arjun/Desktop/gatk-4.1.7.0/gatk". I removed "gatk" from the end of path. Previous error "gatk command not found was solved". However, I got another output message "/usr/bin/env:'python':No such file or directory. After some google research I came to know that this message was associated with default python3 installed in my ubuntu 20. I installed python2.7 and made it first choice for the system. Finally, this worked out. Based on my little recent experience, I believe python3 also creates problem in the installation of the gatk4-4.1.7.0. Please correct me if I am wrong. To summarize path to executable 'gatk' and python version were the probable reason for the problem I was facing. Hope this helps to beginners.
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I have a similar problem.
I use ubuntu 20.04
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