Errors in sceasy when converting from RDS Seurat

[quacksawbones]

Hi Folks,

I am getting the following error when I try to use sceasy (0.0.5+galaxy1) to convert from an RDS Seurat object to an AnnData object:

Loading required package: reticulate
Loading required package: SeuratObject
Error in .requirePackage(package) : 
  unable to find required package 'SeuratObject'
Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'SeuratObject'
Execution halted

It looks like the current version of sceasy available does not fetch the necessary R packages (r-reticulate and r-seuratobject). Could we please get these added into the requirements for sceasy for 0.0.5 and any future versions of this tool?

Thanks folks,

[pcm32]

I guess that this will be a problem on new installations that rely on conda for deps. If you are relying on docker or singularity containers, this shouldn't happen (as Galaxy will use the container created back then) - I would suggest that you use these instead of conda as it will save you many issues with older conda packages trying to install newer deps. The issue here is that the Seurat dependency on the sceasy conda side is probably not pinned, and hence picking up now Seurat 4 instead of 3, for which the package wasn't developed AFAIK. I suspect that version 0.0.7 must be pinned to Seurat <4, which would avoid this.

[pcm32]

Yes, in the container (built back in the day) it uses Seurat 3.1.5.