Hi all, Has anyone come across this?

apptainer-suid

no longer being installable.

Hit:7 <https://ppa.launchpadcontent.net/apptainer/ppa/ubuntu> resolute InRelease
  Reading package lists...
  Building dependency tree...
  Reading state information...
  16 packages can be upgraded. Run 'apt list --upgradable' to see them.

  WARNING: apt does not have a stable CLI interface. Use with caution in scripts.

  Reading package lists...
  Building dependency tree...
  Reading state information...
  Error: Unable to locate package apptainer-suid
  Error: Process completed with exit code 100.

This is stopping all singularity jobs on sanger-tol/nf-core-modules as well as pipeline PR’s into main branches. I can’t see the same issue anywhere else though, so pretty confused and i’ve run out of ideas.

Do you run this in some form of cloud? The PPA still contains a

apptainer-suid

package that seems to be found by

apt install apptainer-suid

, so I’d suspect some cache issue.

This is running on GitHub. I found it to, after the initial panic thinking it got removed. GitHub should be nuking the whole thing per run right?

Yes, each run should get a fresh instance (one can do thing to carry caches over, but that seems weird here).

Have you ensured you are running

apt update

?

Definitely running apt update github.com/sanger-tol/nf-core-modules/…/workflow

Well assuming that is up to date with the version that’s in the

nf-core/modules

repo, then it doesn’t seem like there is any issue in that repo with singularity jobs

That’s what is sending me in circles. We’re using the nf-core workflows, we updated them yesterday to java 25 and python 3.15 (not that they should do anything in this case), but singularity still fails out.

nf-core

runs on ubuntu 24 AFAICT and you are on

26.04

. The runners in

nf-core

are also not github runners but rather from

runs-on

Possible there is some issue there

A colleague has just sent me github.com/spinalcordtoolbox/spinalcordtoolbox/pull/5345 Looks like this group had a similar issue with the apptainer setup. They had to roll back to 24.04 rather than latest

That’s a rather different situation from what you have (an external action that assumes things vs your script at https://github.com/sanger-tol/nf-core-modules/blob/main/.github/actions/nf-test-action/action.yml#L48).

I assume that this hit

nf-core

at some point as following that issue back you find this from @mashehu : github.com/eWaterCycle/setup-apptainer/issues/72

Yes, for the pipelines it looks like it’s fixed it - A colleague is running it on their pipelines at the minute. The nf-core-modules repo likely needs a different fix

This is something I would assume to resolve itself after a while. One might also consider changing your action so it doesn’t try to update directly when adding the PPA, but it seems to be an external thing that you notice.

Looks like maybe in modules we setup

apptainer

manually and have 24.04 runners so there would be no issue. Pipelines CI uses the

eWaterCycle

action to setup apptainer - which I would guess the issue that Matthias opened resolved the problems for 26.04? So you maybe either need to change your CI in your modules clone or downgrade your runners to 24.04

On it 🫡 Thank you both for the help

They do it in the repo-internal action linked above and I don’t see anything that should need changing.

@Jim Downie got it over the line, looks to be working now. github.com/sanger-tol/nf-core-modules/pull/313

Yeah I just tested the “manual” install steps used in the module repo use in a 26.04 container and I have no idea why it doesn’t work on the runner, I had no issues there

Hi, I’m having the same issue with the #C07Q8HNU4FK pipeline: github.com/nf-core/stableexpression/…/129986439629 Should I apply the same fix as mentionned above? github.com/sanger-tol/nf-core-modules/pull/313/changes