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Docker issue gatingset_to_flowjo #162
Description
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 `
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