gs-to-flowjo Singularity issue

[ramyar1993]

Hi,

I am trying to use singularity to convert gating sets to workspace files to use on FlowJo. Here's the line of code I am using to do this:

singularity run -B ./gs_manual:/gs -B ./LLFS_wsp:/out docker://rglab/gs-to-flowjo:devel --cytolib-version --src=/gs --dest=/out/test.wsp

This code runs without any error but does not produce any output wsp files. I realized that gs_manual is not getting recognized as a directory with the .gs, .h5 and .pb files. When I tried to list the files in the gs folder on the singularity shell, I do not get any output:

ramas063@cn2001 [/panfs/roc/groups/15/thyagara/ramas063] % singularity shell ./gs-to-flowjo_devel.sif -B ./gs_manual:/gs -B ./HRS_wsp:/out
Singularity> ls /gs 
Singularity> ls /out

When I try to list files for the ./gs_manual directory instead of the referenced gs folder in the shell command, I still have the three files:

Singularity> ls ./gs_manual
20210127_LLFS_SAMPLES_HB_Group1_23920440_007.fcs.h5  20210127_LLFS_SAMPLES_HB_Group1_23920440_007.fcs.pb  3da10de7-5948-460f-808a-f738bb0a72db.gs

When I tried load_gs:

> load_gs("./gs_manual")
A GatingSet with 1 samples

Please let me know if you have any ideas about solving this issue. Thanks so much!

My R sessionInfo() is below:

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /panfs/roc/msisoft/R/4.1.0/lib64/R/lib/libRblas.so
LAPACK: /panfs/roc/msisoft/R/4.1.0/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] forcats_0.5.1            stringr_1.4.0            purrr_0.3.4
 [4] readr_2.1.2              tidyr_1.2.0              tibble_3.1.6
 [7] tidyverse_1.3.1          dplyr_1.0.8              ggcyto_1.19.1
[10] flowWorkspace_4.7.1      ncdfFlow_2.39.0          BH_1.78.0-0
[13] RcppArmadillo_0.10.8.1.0 flowCore_2.7.1           ggplot2_3.3.5
[16] CytoML_2.7.1             flowWorkspaceData_3.1.0  data.table_1.14.2
[19] openCyto_2.5.4

loaded via a namespace (and not attached):
  [1] colorspace_2.0-3    ellipsis_0.3.2      mclust_5.4.9
  [4] cytolib_2.7.4       corpcor_1.6.10      fs_1.5.2
  [7] base64enc_0.1-3     rstudioapi_0.13     clue_0.3-60
 [10] hexbin_1.28.2       IDPmisc_1.1.20      fansi_1.0.2
 [13] mvtnorm_1.1-3       lubridate_1.8.0     xml2_1.3.3
 [16] splines_4.1.0       R.methodsS3_1.8.1   mnormt_2.0.2
 [19] robustbase_0.93-9   jsonlite_1.8.0      broom_0.7.12
 [22] cluster_2.1.2       dbplyr_2.1.1        png_0.1-7
 [25] R.oo_1.24.0         graph_1.70.0        rrcov_1.6-2
 [28] compiler_4.1.0      httr_1.4.2          rainbow_3.6
 [31] backports_1.4.1     assertthat_0.2.1    Matrix_1.3-3
 [34] cli_3.2.0           tools_4.1.0         gtable_0.3.0
 [37] glue_1.6.2          Rcpp_1.0.8          Biobase_2.52.0
 [40] cellranger_1.1.0    vctrs_0.3.8         rvest_1.0.2
 [43] lifecycle_1.0.1     gtools_3.9.2        XML_3.99-0.9
 [46] DEoptimR_1.0-10     zlibbioc_1.38.0     MASS_7.3-54
 [49] scales_1.1.1        RProtoBufLib_2.5.1  hms_1.1.1
 [52] parallel_4.1.0      RBGL_1.68.0         RColorBrewer_1.1-2
 [55] yaml_2.3.5          curl_4.3.2          aws.signature_0.6.0
 [58] gridExtra_2.3       stringi_1.7.6       latticeExtra_0.6-29
 [61] S4Vectors_0.30.2    pcaPP_1.9-74        flowClust_3.29.1
 [64] BiocGenerics_0.38.0 hdrcde_3.4          flowViz_1.53.0
 [67] rlang_1.0.2         pkgconfig_2.0.3     matrixStats_0.61.0
 [70] bitops_1.0-7        pracma_2.3.8        fda_5.5.1
 [73] lattice_0.20-44     ks_1.13.4           tidyselect_1.1.2
 [76] deSolve_1.30        plyr_1.8.6          magrittr_2.0.2
 [79] R6_2.5.1            generics_0.1.2      DBI_1.1.2
 [82] pillar_1.7.0        haven_2.4.3         withr_2.5.0
 [85] RCurl_1.98-1.6      modelr_0.1.8        crayon_1.5.0
 [88] KernSmooth_2.23-20  utf8_1.2.2          tmvnsim_1.0-2
 [91] tzdb_0.2.0          fds_1.8             aws.s3_0.3.21
 [94] jpeg_0.1-9          grid_4.1.0          readxl_1.3.1
 [97] Rgraphviz_2.36.0    reprex_2.0.1        digest_0.6.29
[100] R.utils_2.11.0      flowStats_4.5.3     RcppParallel_5.1.5
[103] stats4_4.1.0        munsell_0.5.0

108

[ramyar1993]

I just realized that the images are being maintained here. The singularity execution works now with this new image.

However, it would be useful if this was updated in the Cytoverse documentation. This page still refers to the docker image on the RGLab docker Hub page.

[mikejiang]

Thank you for reporting the issue, I have updated the link