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Anyone else having an issue trying to run VEP inside a Singularity container?

@gau we run it locally or in docker. what sort of issues are you running into?

@tor
An issue within VEP.
It seems to be working well with GRCh37, but fails with GRCh38...

@gau Ah, we're still stuck on GRCh37 :(

That error seems odd for using a different build version though. Seems like it's mis-detecting the terminal status for some reason.

Might be something failing elsewhere and just showing up as that. That's the best I can guess from afar.

Is that your source image, or something with the solution?

@tor This could be our solution.
Our source image is the one provided by ensembl: willmclaren/ensembl-vep:release_92

But that was probably a not the best idea ever...

@tor Finally manage to fix it, it seems that the VEP 92 was not working with Singularity 2.5.
We managed to fix everything by updating our tools: github.com/SciLifeLab/Sarek/pu

@gau Ah, nice. I kinda dislike solutions that are just "upgrade to next version" without the why personally, but the important thing is it works.

We're still stuck v2.5.0 in cluster, though hoping to get the new 3.0 in there soon to support the new .sif format.

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