Wave and Singularity

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1

Hi all, I really enjoyed the summit and I am very happy we now have a community forum!

After having seen the wave-cli demo by @paolo, I have been experimenting a bit with it and, especially, singularity. I am using singularity-ce version 3.9.5.

As from the demo and the docs, I used the --singularity option freezing the image and specifying a build repo and that worked:

> singularity exec $(wave --conda-package star=2.4.0j --conda-package sambamba=0.7.1 --singularity --freeze --build-repo docker.io/emi80/wave-build --await) STAR --version
INFO:    Downloading oras image
INFO:    Converting SIF file to temporary sandbox...
STAR_2.4.0j
INFO:    Cleaning up image...

Then, I was wondering whether I could directly create a container from the image stored in the wave server (I know that the built images are cleaned up, but I think this could be useful for quick-building images or for on-prem wave servers):

> singularity exec docker://$(wave --conda-package star=2.4.0j --conda-package sambamba=0.7.1 --await) STAR --version
INFO:    Using cached SIF image
INFO:    Converting SIF file to temporary sandbox...
FATAL:   "STAR": executable file not found in $PATH
INFO:    Cleaning up image...

It almost worked but it seems like using the exec singularity command (mimicking Nextflow behavior) the tools are not found in $PATH. Using run would solve the issue as the micrimamba Docker image as a default SHELL command that configures the conda environment. Using the full path of the tools would work:

❯ singularity exec docker://$(wave --conda-package star=2.4.0j --conda-package sambamba=0.7.1 --await) /opt/conda/bin/STAR --version
INFO:    Using cached SIF image
INFO:    Converting SIF file to temporary sandbox...
STAR_2.4.0j
INFO:    Cleaning up image...

I was wondering whether this is a bug and, in case, if it could be fixed by:

  • prepending the image returned by Wave with docker:// when a singularity image is requested and thus not requiring a freeze

and either:

  • updating the micromamba Docker image to work with singularity exec
  • use singularity run in Nextflow (though this could possibly have an unexpected impact on existing pipelines)

P.S. Tried with singularity 4 and the --oci flag but AFAIU it still needs the docker:// prefix and does not help either:

❯ singularity exec --oci docker://$(wave --conda-package star=2.4.0j --conda-package sambamba=0.7.1  --await) STAR --version
INFO:    Using cached OCI-SIF image
2023-10-22T09:04:00.000543593Z: executable file `STAR` not found in $PATH: No such file or directory

Thanks!

2

It almost worked but it seems like using the exec singularity command (mimicking Nextflow behavior) the tools are not found in $PATH

Because the Singularity build exports the tool mamba bin path, while that’s not needed by Docker

Also local Singularity conversion is not a good idea for non-freezed containers because it can convert multiple times the same image just having a different name.

This will be addressed by the support for Singularity 4.

3

Thanks @paolo for the quick reply.

I see, so the same image but with a different name will have a different hash and would need to be reconverted since the “old” cache would not be valid…

Great! Any expected timeframe for that?

4

It should be pretty simple. You may expect it in the upcoming weeks. you can help us figure out why Singularity 4 image is not building GitHub - singularityhub/singularity-docker at v4.0.0

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5

I updated the Dockerfile and now it builds.

GitHub - emi80/singularity-docker at v4.0.0 - it might need some clean-up but it works :partying_face:

I will make a PR to the original repo as well.

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7

Awesome, well done!

(adding some random text otherwise the forum does not allow me to reply)

1 Like
8

Hey @paolo!

Thanks to the fast response time of @vsoch we now have various singularity 4.0.1 Dockerfiles working for amd64 and arm.

Cheers!

9

Thanks Emilio! look into next step: