bioconda-recipes: Singularity contains built from bioconda have broken /etc/resolv.conf

A test with a container built using singularity build from the Docker images on quay.io using Singularity 2.5.2.

$ singularity exec /tools/containers/sra-tools-2.9.1_1--h470a237_0.simg ping www.google.com
ping: bad address 'www.google.com'
$ singularity exec /tools/containers/sra-tools-2.9.1_1--h470a237_0.simg cat /etc/resolv.conf
cat: can't open '/etc/resolv.conf': No such file or directory
$ singularity exec /tools/containers/sra-tools-2.9.1_1--h470a237_0.simg ls -ld /etc/resolv.conf
lrwxrwxrwx    1 root     root            18 Feb 27  2014 /etc/resolv.conf -> ../tmp/resolv.conf

This is mentioned by @vsoch as a Weirdo File. It is not clear where the link to ../tmp/resolv.conf comes from.

About this issue

Original URL
State: closed
Created 6 years ago
Comments: 45 (35 by maintainers)

Most upvoted comments

@nfancy Regarding the /etc/resolv.conf warning: I’ve seen this error in old container images that were built before the Biocontainers base image update mentioned in https://github.com/bioconda/bioconda-recipes/issues/11583#issuecomment-830099492. I don’t have practical experience with Nextflow; does your workflow define an old container image(s)?

The “FATAL” error looks like it could be a site-specific Singularity configuration issue; I’d suggest reaching out to your local sysadmin and/or Nextflow experts for guidance. This issue could be related.

nathanweeks on Feb 6, 2023

I think this one can now be closed, please reopen if this is still an issue.

bgruening on Jan 22, 2022

According to a discussion with @mbargull on Gitter, this is due to be resolved early in 2021. In the meantime, I will note the use of extended-base image simply to get around this issue in:

irida-uploader PR: #25378
ensembl-vep PR: #25393
entrez-direct PR: #26524

pvanheus on Feb 2, 2021

@vsoch is it not linked on the dockerhub page? We should add it to some documentation if not.

@nathanweeks yes exactly. That should still work I hope: https://galaxy-lib.readthedocs.io/en/latest/topics/mulled.html?highlight=mulled#building-docker-containers-for-local-conda-packages

You should be able to specify the base image via command line args. If not this should get you started: https://github.com/galaxyproject/galaxy-lib/pull/148

Sorry, in a train with terrible internet. A nice Easter holiday for you all!

bgruening on Apr 19, 2019