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[desmodus1984]

Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.6.1/docs/FAQ.md: Yes

Describe the issue: I can't pull the container using singularity.

Setup

• Operating system: Ubuntu
• Installation method (Docker, built from source, etc.): tried with singularity My system has singularity installed, I tried getting the container but it failed:

I used this code

BIN_VERSION="1.6.1"
singularity pull docker://google/deepvariant:"${BIN_VERSION}"

and It got several warning messages:

WARNING: pull for Docker Hub is not guaranteed to produce the WARNING: same image on repeated pull. Use Singularity Registry WARNING: (shub://) to pull exactly equivalent images. /usr/bin/env: ‘python’: No such file or directory Cleaning up... ERROR: pulling container failed!

I was thinking of installing DeepVariant with conda, but the version in conda is 1.5.0, and I was told to always run the most up-to-date one.

[kishwarshafin]

Hi @desmodus1984 ,

I just checked our singularity solution and it works on a n2-standard-64 GCP machine. Without knowing much about your system, my guess is it's probably something related to how singularity is installed in your system? Are you on an HPC?

[desmodus1984]

Hi @kishwarshafin

I did install Singularity in a conda environment and then I used the singularity installed in the HPC, and in both systems I couldn't download the container.

[kishwarshafin]

@desmodus1984 ,

Can you verify this issue is specific to DeepVariant and not your system? Can you run:

singularity pull docker://ubuntu:latest

And see if you are able to download that?

[kishwarshafin]

Closing this for no activity. Feel free to reopen if you need further help.