Skip to content

Docker issue gatingset_to_flowjo #162

@klai001

Description

@klai001

Hi all
thanks for the useful package
i am trying to mainly convert gs to flowjo workspace.
but i dont understand this docker error.
I've downloaded through BioC delevel version and also tried with the latest github version

library(flowWorkspace)
library(openCyto)
library(CytoML)


wsp <- list.files(".", pattern = "template_for_clean_samples.wsp")
ws<-open_flowjo_xml(paste0(getwd(), "/", wsp), name = 1, sample_names_from = "sampleNode")
gs <- flowjo_to_gatingset(ws, name = 1, path = getwd())

flowWorkspace::gs_get_pop_paths(gs, path = "full")
gs_pop_get_count_with_meta(gs)
gs_pop_get_data(gs)
setwd('.')
outFile <- tempfile(fileext = "test.wsp")
gatingset_to_flowjo(gs, outFile)

I have used the docker pull as advised.
Using docker image public.ecr.aws/x4k5d9i7/cytoverse/gs-to-wsp:latest to write FlowJo workspace...
Error in gatingset_to_flowjo(gs, outFile) :
docker: invalid reference formatRun 'docker run --help' for more information
`> sessionInfo()
R version 4.5.0 RC (2025-04-04 r88118 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)

Matrix products: default
LAPACK version 3.12.1

locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

time zone: Europe/London
tzcode source: internal

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] CytoML_2.19.3 openCyto_2.19.2 flowWorkspace_4.19.1 BiocManager_1.30.25

loaded via a namespace (and not attached):
[1] generics_0.1.3 lattice_0.22-6 digest_0.6.37 magrittr_2.0.3
[5] evaluate_1.0.3 grid_4.5.0 RColorBrewer_1.1-3 fastmap_1.2.0
[9] jsonlite_2.0.0 ggcyto_1.35.0 plyr_1.8.9 graph_1.85.3
[13] gridExtra_2.3 scales_1.3.0 XML_3.99-0.18 Rgraphviz_2.51.9
[17] cli_3.6.4 rlang_1.1.5 RProtoBufLib_2.19.0 Biobase_2.67.0
[21] munsell_0.5.1 yaml_2.3.10 cytolib_2.19.3 parallel_4.5.0
[25] tools_4.5.0 ncdfFlow_2.53.1 dplyr_1.1.4 colorspace_2.1-1
[29] ggplot2_3.5.1 BiocGenerics_0.53.6 vctrs_0.6.5 R6_2.6.1
[33] matrixStats_1.5.0 stats4_4.5.0 lifecycle_1.0.4 S4Vectors_0.45.4
[37] flowCore_2.19.0 RBGL_1.83.0 pkgconfig_2.0.3 pillar_1.10.2
[41] hexbin_1.28.5 gtable_0.3.6 data.table_1.17.0 glue_1.8.0
[45] Rcpp_1.0.14 flowClust_3.45.0 xfun_0.52 tibble_3.2.1
[49] tidyselect_1.2.1 rstudioapi_0.17.1 knitr_1.50 htmltools_0.5.8.1
[53] rmarkdown_2.29 compiler_4.5.0 `

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions