Please provide instructions on how to use singularity to run GLnexus

dnanexus-rnd / GLnexus

Scalable gVCF merging and joint variant calling for population sequencing projects

Apache License 2.0

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Open hoyonh opened 1 year ago

hoyonh commented 1 year ago

I would appreciate instructions on how to run GLnexus using singularity - the format used by the likes of Deepvariant would be really welcome - see link https://github.com/google/deepvariant/blob/r1.4/docs/deepvariant-quick-start.md (see section: Notes on Singularity)

Thank you very much for your help!

lvclark commented 1 year ago

I just happened upon this issue while looking for something else. I had luck today with

singularity pull docker://ghcr.io/dnanexus-rnd/glnexus:v1.4.1

There's also a singularity image hosted by Galaxy, but it doesn't seem to have jemalloc installed. So I went with the official Docker one.