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langmead-lab / monorail-external

examples to run monorail externally
MIT License
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singularity pull docker not working #28

Closed pabloacera closed 5 months ago

pabloacera commented 5 months ago

Hi, any idea why?

sudo singularity pull docker://quay.io/broadsword/recount-unify:1.1.1
[sudo] password for paceramateos:
Sorry, try again.
[sudo] password for paceramateos:
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
INFO:    Fetching OCI image...
9.3MiB / 9.3MiB [===================================================================================================================================================================================================================] 100 % 0.0 b/s 0s
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INFO:    Extracting OCI image...
FATAL:   While making image from oci registry: error fetching image to cache: while building SIF from layers: packer failed to pack: while unpacking tmpfs: error unpacking rootfs: unpack entry: opt/conda/pkgs/certifi-2018.11.29-py37_0/lib/python3.7/site-packages/certifi/__init__.py: link: no such file or directory

singularity --version
singularity-ce version 4.1.0-rc.1+4-g69b6809e8
ChristopherWilks commented 5 months ago

Hi @pabloacera,

I haven't downloaded images via singularity in a while, however, when I just tried with singularity 4.0.3 the recount-unify:1.1.1 sif file was created without issue using the same command as you (sans the sudo).

When I have some additional time I'll try with 4.1.0-rc.1 and see if it's a version specific issue. At the same time, if you have access to a slightly older singularity installation I'd suggest trying that.

Chris

pabloacera commented 5 months ago

Hi @ChristopherWilks,

Thanks, I downgraded the singularity to 4.0.3 and it works now. Cheers