Singularity container creation

[kdavydzenka]

It would be helpful to have a Singularity container (image) of your package!

[mdbarnesUCSD]

Thanks for the feedback! This is something that we are hoping to have in a future release. We will update here when it is ready.

[lculibrk]

I've built a docker image for the SigProfiler tools. I haven't extensively tested it, but it builds just fine. GRCh37 and GRCh38 are installed.

https://hub.docker.com/repository/docker/lculibrk/sigprofiler

singularity pull docker://lculibrk/sigprofiler:latest

[lculibrk]

Update on my previous comment,

The container runs into the errors outlined here: #247

I'll try to rebuild and see if that helps. @mdbarnesUCSD , if this is an issue inherent to containerizing the SigProfiler suite, is there any guidance you can provide to workaround the issue? Happy to share the Dockerfile too.

[mdbarnesUCSD]

There are some issues that originate from the default behavior for SigProfilerMatrixGenerator and SigProfilerPlotting because of how they save and load files from site-packages. There are some updates that we are rolling out that enable this behavior to change by adding a parameter "volume" for a user specified location. SigProfilerExtractor will also need to be updated to utilize these changes before a singularity container will work. Here are the recent updates to SigProfilerAssignment.

[kdavydzenka]

I tested the tool inside your Singularity container and it runs into the same errors as yours: #247

[FerriolCalvet]

Hi!
I want to use SigProfilerExtractor from a container and I was wondering if this error has been solved in some way or which would be the best container to use for that. Thanks in advance!