Garnett outdated libraries

[hexhowells]

Running the tool Garnett - classify cells in a Galaxy workflow produces the following error:

Error in checkSlotAssignment(object, name, value) : 
  ‘reducedDims’ is not a slot in class “SingleCellExperiment”
Calls: classify_cells
Execution halted

Here is a Galaxy workflow replicating the issue:
https://humancellatlas.usegalaxy.eu/u/hexhowells/h/garnett-reduceddims-error

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This appears to be an issue with an older version of the monocle3 library as it was raised in their Github a while ago: cole-trapnell-lab/monocle3#272 seems the issue was resolved in an updated version of monocle3.

I have run the classify_cells function locally on my machine with the same data used in the workflow using the most recent versions of monocle3 (monocle3_1.3.1) and garnett (garnett_0.2.20) so there seems no issue with the data.

[nomadscientist]

@pcm32 I'm wondering if we should remove these tools from the https://singlecell.usegalaxy.eu instance given that they don't currently function as a workflow, the original tools are quite old, and there's not much resource for keeping them updated?

[pcm32]

I think that if we remove them, they will never get to be on a workflow. Very likely most galaxy tools have never made it to a very reused workflow for that matter.

[pcm32]

So the question here is what happens if we update those underlying tools, how much effort is required and can someone do it?

[nomadscientist]

I can submit it as an intern role like Morgan had last year, so if you were to update it, I can probs get someone testing it for the summer latest as a nice wee project