Problem installing/testing gatk-4.1.7.0

Question

[arjun.upadhaya]

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. Is the problem related to path issue. If so please help me to figure out.

Answer 1

[jordi.planells]

Have you tried with conda? It is a package manager that will save you a lot of time, as the programs are ready to install and conda takes cares of dependencies (added a link so you can follow their installation guide).

You will need to install conda. Then you can create a new environment and install gatk as following:

1.Create a new environment

conda create -n my_new_environment

2.Activate environment and install

conda activate my_new_environment

conda install -c bioconda gatk4

I hope the answer helps! Best,

Jordi

[arjun.upadhaya]

Thank you, Jordi for the quick response. Let me try it.

Answer 2

[Pierre Lindenbaum]

The PATH should point to the directory, not to the executable. try

export PATH=$PATH:/home/arjun/Desktop/gatk-4.1.7.0

[arjun.upadhaya]

Thank you for quick response, Pierre! Now I am getting. arjun@arjun-VirtualBox:~$ gatk --help

/usr/bin/env: ‘python’: No such file or directory

Some time ago, I installed python 2.7 although I had python3 installed earlier. Now, I have both. Removing executibable from PATH also did not help. export PATH=$PATH:"/home/arjun/Desktop/gatk-4.1.7.0" But still I am assuming it has something to do with path or may be I am wrong.