Hello!

I am new to bionformatics/GATK, so I'm hoping someone with experience can help me identify what I am doing wrong.

I believe I have sucessfully installed BWA, SAMtools, and PICARD (although it was challenging given the walk through should be updated: https://gatk.broadinstitute.org/hc/en-us/articles/360041320571--How-to-Install-all-software-packages-required-to-follow-the-GATK-Best-Practices), however when I try to install GATK I have run in to many difficulties.

First, I downloaded the package directly as per the intrsuctions. The file I have on my computer is a zip file labelled "gatk-4.1.6.0.zip". The next steps in the walk through states this code "

    tar xjf GenomeAnalysisTK-3.3-0.tar.bz2 

should unpack the package, however this doesn't work (I suspect because this is not a tar file?).

Here is the code and error:

(ENVNAME) mh_user@MicrobiomeHelper:~$ conda env create -f /home/mh_user/gatk-4.1.6.0.zip
Command 'dirname' is available in '/usr/bin/dirname'
The command could not be located because '/usr/bin' is not included in the PATH environment variable.
dirname: command not found
Command 'dirname' is available in '/usr/bin/dirname'
The command could not be located because '/usr/bin' is not included in the PATH environment variable.
dirname: command not found

EnvironmentFileExtensionNotValid: '/home/mh_user/gatk-4.1.6.0.zip' file extension must be one of '.txt', '.yaml' or '.yml'

Given I could not successfully unpack this package, I tried creating a DOCK (although I don't necessarily understand the concept and further struggle understanding what  shell is and how to exactly use them). I followed instructions posted here: https://hub.docker.com/r/broadinstitute/gatk/ and successfully received the "Hello from Docker!
This message shows that your installation appears to be working correctly.

To generate this message, Docker took the following steps:
1. The Docker client contacted the Docker daemon.
2. The Docker daemon pulled the "hello-world" image from the Docker Hub.
(amd64)
3. The Docker daemon created a new container from that image which runs the
executable that produces the output you are currently reading.
4. The Docker daemon streamed that output to the Docker client, which sent it
to your terminal".

However, when I continued I got this error after running the code below: 

) mh_user@MicrobiomeHelper:~$ docker --version
Docker version 19.03.8, build afacb8b7f0

(ENVNAME) mh_user@MicrobiomeHelper:~$ docker pull broadinstitute/gatk:4.1.3.0
Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post http://%2Fvar%2Frun%2Fdocker.sock/v1.40/images/create?fromImage=broadinstitute%2Fgatk&tag=4.1.3.0: dial unix /var/run/docker.sock: connect: permission denied

Any help and advice is greatly appreciated!

Taylor