Docker daemon: Is the docker daemon running?
Entering edit mode
9 weeks ago
c.eskiw ▴ 10

Good day all,

I am trying to eventually run the Genome Analysis Tool Kit. However, I am a Linux user and GATK does not run directly from the Windows version of Docker Desktop. I have been trying to install Docker Desktop through Ubuntu. Some nice tutorials online; however, these are failing. I am not using Ubuntu desktop but the terminal window (Ubuntu 22.1).

I have followed the installation instructions listed here:

I have installed with:

sudo apt-get install sudo apt install "/mnt/c/Users/chris/Downloads/docker-desktop-4.14.1-amd64.deb" 

All good.

The next set of instructions has confounded me:

There are a few post-install configuration steps done through the post-install script contained in the deb package.

The post-install script:

Sets the capability on the Docker Desktop binary to map privileged ports and set resource limits.
Adds a DNS name for Kubernetes to /etc/hosts.
Creates a link from /usr/bin/docker to /usr/local/bin/com.docker.cli

I have not completed this as there is no /bin/docker file

The error message here is:

Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?

I have been through multiple help pages and fixes but I am still getting this message.

Any fix for this would be great or another way I could use GATK in the linux/ubuntu environment would be great.


Ubuntu Docker GATK • 449 views
Entering edit mode
9 weeks ago
zorbax ▴ 530

If you are trying to install Docker Desktop Linux on Windows WSL with Ubuntu, it would be better to install the Windows version of Docker Desktop and enable the WSL 2 backend engine. Otherwise, you will be using virtual machines instead of a Linux kernel built by Microsoft.

Entering edit mode

This worked! Thank you for the suggestion.

Entering edit mode
9 weeks ago

If you are working on Unix I would recommend using Singularity containers. A whole lot less hassle than Docker.


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