Where is my GATK4 ?

Answered

Follow

MianQi

• December 20, 2021 10:15
• Edited

I have installed java 8 and docker on Ubuntu 20.04 as it was told here:

1.https://gatk.broadinstitute.org/hc/en-us/articles/360036194592-Getting-started-with-GATK4

2.https://gatk.broadinstitute.org/hc/en-us/articles/360035889991

and I have got prompt as these:

Using default tag: latest
latest: Pulling from broadinstitute/gatk
Digest: sha256:5c8ad33becf8541ede410de4c99b861ae13bbb0a2dfa7501dcd758be8fc3f36d
Status: Image is up to date for broadinstitute/gatk:latest
docker.io/broadinstitute/gatk:latest

but when I went to run it by:

sudo docker run -it broadinstatitute/gatk:latest

I got these prompt:

Unable to find image 'broadinstatitute/gatk:latest' locally
docker: Error response from daemon: pull access denied for broadinstatitute/gatk, repository does not exist or may require 'docker login': denied: requested access to the resource is denied.
See 'docker run --help'.

and I couldn't find the more than 1.7G file I have downloaded, neither in "Downloads" folder, nor in the folder I have run "sudo docker pull broadinstitute/gatk"

when I ran "sudo docker image ls", it was prompted:

REPOSITORY TAG IMAGE ID CREATED SIZE
broadinstitute/gatk latest 032abdb7f192 4 days ago 4.5GB
hello-world latest feb5d9fea6a5 2 months ago 13.3kB

I just want to know where is the image and how could I start to run:

docker run -it broadinstitute/gatk:

 

 

0

• 

  Genevieve Brandt (she/her)

  • January 10, 2022 23:37

  Hi MianQi,

  Thank you for writing into the forum! Let's see if we can get GATK working for you on Docker, since Docker is so convenient.

  Can you see if GATK docker works when you reference a specific GATK version? Here is how I normally use docker:

  docker pull broadinstitute/gatk:4.2.4.1
  docker run -it broadinstitute/gatk:4.2.4.1

  Let me know if this works and if you have any further questions!

  Genevieve

  0

  Comment actions Permalink

Please sign in to leave a comment.