search

AusARG / pipesnake

ausarg/pipesnake is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data.
MIT License
7 stars 2 forks source link

Docker-In-Docker failure #11

Open njdowdy opened 5 months ago

njdowdy commented 5 months ago

Description of the bug

This pipeline is not compatible with Docker-in-Docker using Docker version >=26 due to a deprecation of the schema that the BLAT image uses.

More info: https://docs.docker.com/engine/deprecated/#pushing-and-pulling-with-image-manifest-v2-schema-1

To my knowledge, the only fix is for the BLAT maintainer to update their image to meet the new standards or to pin the supported docker version to 25 or earlier.

Command used and terminal output

[DEPRECATION NOTICE] Docker Image Format v1 and Docker Image manifest version 2, schema 1 support is disabled by default and will be removed in an upcoming release. Suggest the author of docker.io/feathj/fake-sqs:latest to upgrade the image to the OCI Format or Docker Image manifest v2, schema 2. More information at https://docs.docker.com/go/deprecated-image-specs/

Relevant files

No response

System information

No response

IanGBrennan commented 5 months ago

Hey there, sorry for the slow reply on this. Could you explain a bit more about why this might be important? I am not familiar with docker-in-docker usage, and so curious if this is something like to become an issue, or if it's a less common practice. Cheers Ian

njdowdy commented 5 months ago

I have an HPC that runs docker containers. I need to run the Nextflow environment in a docker container, which itself uses the PipeSnake docker container, necessitating the docker-in-docker nesting. To resolve the above issue, I pulled an image of Docker pinned to version 25, installed Nextflow within the container, and then continued with the PipeSnake installation instructions to get around the above problem. So, just a mild frustration.

The real "solution" is for the BLAT maintainer to maintain their Docker image or for PipeSnake to use an alternative BLAT image that follows Docker's new standards around Docker Image manifest/schema rules. I'm not sure if you all were interested in looking for an alternative BLAT image that conforms to these standards, or if this comment would simply serve as an FYI to the community in case they run into this problem too.