Problem encountered when running the code in containers

[superjw]

Hi there,

Just wondering if you could set this dir as somewhere else like a "temp working directory"?

https://github.com/AlexandrovLab/SigProfilerAssignment/blob/7fef91c5e1c898ccad482e4a3a783bcef53366ec/SigProfilerAssignment/DecompositionPlots/PlotDecomposition.py#L48

The current setting works fine when you have "write permission" to the library dir. However, if you put it into a container it will unlikely to function because the library path will be "read-only" most of the times.

Thanks,

Jingwei

[mdbarnesUCSD]

Hi @superjw,

Thanks for reaching out. We will be looking to modify this behavior in a future release.

[me-nobody]

Hi, when to use this parameter, collapse_to_SBS96=True?

[nservant]

Hi @mdbarnesUCSD, Any news on this topic ? It would be really great to be able to profile annotation files which are intall in another folder ... as already done with the volume parameter here ; https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/issues/131 Thanks

[mdbarnesUCSD]

Hi @nservant and @superjw,

The volume parameter has been added as well as support for the environmental variable "SIGPROFILERASSIGNMENT_VOLUME". The environmental variable takes precedence over the parameter and should be a directory that the user has read/write access to.