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RGLab / CytoML

A GatingML Interface for Cross Platform Cytometry Data Sharing
GNU Affero General Public License v3.0
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gatingset_to_flowjo hangs #157

Closed Biomiha closed 3 months ago

Biomiha commented 4 months ago

Hi,

I've been trying to export a gatingset to flowjo using Docker. I have pulled the latest image from: public.ecr.aws/x4k5d9i7/cytoverse/gs-to-wsp:latest.

If I try to export the example gs

library(CytoML)
library(flowWorkspace)

dataDir <- system.file("extdata",package="flowWorkspaceData")
gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE))
#flowJo
outFile <- tempfile(fileext = ".wsp")
gatingset_to_flowjo(gs = gs, outFile = "test.wsp")

I get the following:

WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested

And it hangs forever, without actually exporting the workspace.

Alternatively, I can successfully export to cytobank xml using:

gatingset_to_cytobank(gs = gs, outFile = "test_cytobank.xml") # this works fine

Any particular reason the gatingset_to_flowjo would hang? I am on a Macbook M1, hence the platform warning.

Thanks

Biomiha commented 3 months ago

This is to do with conflicting platforms on a Mac. Have not found a way of fixing even by specifying the platform and running rossetta.