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EichlerLab / pav

Phased assembly variant caller
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apptainer run error #59

Open jeffchen2000 opened 2 months ago

jeffchen2000 commented 2 months ago

Hi EichlerLab

apptainer is updated version of singularity

when I run it, I got error. thanks for comments!

apptainer run --bind "$(pwd):$(pwd)" library://becklab/pav/pav:latest -c 16 FATAL: Unable to handle library://becklab/pav/pav:latest uri: remote has no library client

paudano commented 2 months ago

This looks like new behavior with apptainer. There's a good explanation I found in the Max Planck computing documentation: https://docs.mpcdf.mpg.de/bnb/211.html#notes-on-the-sylabs-cloud-endpoint

I'll need to update the documentation in PAV. Thanks for pointing this out.

jeffchen2000 commented 2 months ago

thanks a lot paudano!!!

it worked with the followings: apptainer remote add --no-login SylabsCloud cloud.sylabs.io apptainer remote use SylabsCloud apptainer run --bind "$(pwd):$(pwd)" library://becklab/pav/pav:latest -c 16

paudano commented 1 month ago

I am going to leave this open to remind me to update the documentation. I don't need anything else from you. Thank you for reporting this!