Browse code

update docker reference

mikejiang authored on 10/03/2021 00:33:15
Showing 2 changed files

... ...
@@ -24,21 +24,10 @@ GatingSet2flowJo <- function(...){
24 24
 #' @return nothing
25 25
 #' 
26 26
 #' @details 
27
-#' Docker images for \code{gatingset_to_flowjo} will be maintained at https://hub.docker.com/r/rglab/gs-to-flowjo for the \code{cytolib} 
28
-#' package version accompanying each Bioconductor release, as well as a "devel" tagged image for use with the current GitHub development 
29
-#' braches of the RGLab cytometry packages.
27
+#' Docker images for \code{gatingset_to_flowjo} will be maintained at https://gallery.ecr.aws/x4k5d9i7/cytoverse/gs-to-wsp
30 28
 #' 
31
-#' If you are using CytoML from a Bioconductor release, please pull docker image corresponding to the major and minor version returned from
32
-#' \code{packageVersion("cytolib")}, For example, if \code{packageVersion("cytolib")} returns \code{2.0.2}, you should use:
33 29
 #' 
34
-#' \code{docker pull rglab/gs-to-flowjo:2.0}
35
-#' 
36
-#' If you are using CytoML from the current GitHub development branch ("master" branch), please pull the "devel" tagged image. For example:
37
-#' 
38
-#' \code{docker pull rglab/gs-to-flowjo:devel}
39
-#' 
40
-#' You may also specify a particular docker image and tag via the \code{docker_img} argument. If not provided, \code{gatingset_to_flowjo} will
41
-#' search for the correct default image corresponding to your \code{cytolib} version.
30
+#' \code{docker pull public.ecr.aws/x4k5d9i7/cytoverse/gs-to-wsp:latest}
42 31
 #' 
43 32
 #' @examples
44 33
 #' \dontrun{
... ...
@@ -86,8 +75,8 @@ gatingset_to_flowjo <- function(gs, outFile, showHidden = FALSE, docker_img = NU
86 75
     docker_img <- res[2] # The validated image name from check_docker_status()
87 76
     v1 <- packageVersion("cytolib")
88 77
     v2 <- system2("docker", paste0("run ", docker_img, " --cytolib-version"), stdout = TRUE)
89
-    if(v1!=v2)
90
-      warning("docker image '", docker_img, "' is built with different cytolib version of from R package: ", v2, " vs ", v1)
78
+    # if(v1!=v2)
79
+    #   warning("docker image '", docker_img, "' is built with different cytolib version of from R package: ", v2, " vs ", v1)
91 80
     
92 81
     
93 82
     message(paste0("Using docker image ", docker_img, " to write FlowJo workspace..."))
... ...
@@ -137,29 +126,29 @@ check_docker_status <- function(docker_img = NULL){
137 126
   
138 127
   # Determine proper default image for this cytolib version
139 128
   if(is.null(docker_img)){
140
-    base_img <- "rglab/gs-to-flowjo"
141
-    
142
-    # strip last patch numbers
143
-    cytolib_minor_version <- gsub("\\.[^.]*$", "", packageVersion("cytolib"))
129
+    docker_img <- "public.ecr.aws/x4k5d9i7/cytoverse/gs-to-wsp:latest"
144 130
     
145
-    # First try to match cytolib minor version directly to image name
146
-    docker_version_match <- system2("docker", paste0("  image inspect ", paste0(base_img, ":", cytolib_minor_version)), stdout = FALSE, stderr = FALSE)
147
-    if(docker_version_match==0){
148
-      docker_img <- paste0(base_img, ":", cytolib_minor_version)
149
-    }else{
150
-    # Otherwise, check for devel tagged image and see if that minor version matches
151
-      devel_img <- paste0(base_img, ":devel")
152
-      if(system2("docker", paste0("  image inspect ", devel_img), stdout = FALSE, stderr = FALSE) == 0){
153
-        devel_img_version <- system2("docker", paste0("run ", devel_img, " --cytolib-version"), stdout = TRUE)
154
-        if(gsub("\\.[^.]*$", "", devel_img_version) == cytolib_minor_version)
155
-          docker_img <- devel_img
156
-      }
157
-    }
131
+    # # strip last patch numbers
132
+    # cytolib_minor_version <- gsub("\\.[^.]*$", "", packageVersion("cytolib"))
133
+    # 
134
+    # # First try to match cytolib minor version directly to image name
135
+    # docker_version_match <- system2("docker", paste0("  image inspect ", paste0(base_img, ":", cytolib_minor_version)), stdout = FALSE, stderr = FALSE)
136
+    # if(docker_version_match==0){
137
+    #   docker_img <- paste0(base_img, ":", cytolib_minor_version)
138
+    # }else{
139
+    # # Otherwise, check for devel tagged image and see if that minor version matches
140
+    #   devel_img <- paste0(base_img, ":devel")
141
+    #   if(system2("docker", paste0("  image inspect ", devel_img), stdout = FALSE, stderr = FALSE) == 0){
142
+    #     devel_img_version <- system2("docker", paste0("run ", devel_img, " --cytolib-version"), stdout = TRUE)
143
+    #     if(gsub("\\.[^.]*$", "", devel_img_version) == cytolib_minor_version)
144
+    #       docker_img <- devel_img
145
+    #   }
146
+    # }
158 147
   }
159 148
   
160 149
   if(is.null(docker_img)){
161 150
     # Search for a valid default image failed
162
-    return(paste0("No default docker image found matching cytolib version ", packageVersion("cytolib"), ".\n",
151
+    return(paste0("No default docker image found\n",
163 152
                   "Please see help(gatingset_to_flowjo) about pulling the appropriate docker image."))
164 153
   }else{
165 154
     # Try candidate image
... ...
@@ -26,21 +26,10 @@ It is a R wrapper for the docker app
26 26
 (https://hub.docker.com/r/rglab/gs-to-flowjo)
27 27
 }
28 28
 \details{
29
-Docker images for \code{gatingset_to_flowjo} will be maintained at https://hub.docker.com/r/rglab/gs-to-flowjo for the \code{cytolib} 
30
-package version accompanying each Bioconductor release, as well as a "devel" tagged image for use with the current GitHub development 
31
-braches of the RGLab cytometry packages.
29
+Docker images for \code{gatingset_to_flowjo} will be maintained at https://gallery.ecr.aws/x4k5d9i7/cytoverse/gs-to-wsp
32 30
 
33
-If you are using CytoML from a Bioconductor release, please pull docker image corresponding to the major and minor version returned from
34
-\code{packageVersion("cytolib")}, For example, if \code{packageVersion("cytolib")} returns \code{2.0.2}, you should use:
35 31
 
36
-\code{docker pull rglab/gs-to-flowjo:2.0}
37
-
38
-If you are using CytoML from the current GitHub development branch ("master" branch), please pull the "devel" tagged image. For example:
39
-
40
-\code{docker pull rglab/gs-to-flowjo:devel}
41
-
42
-You may also specify a particular docker image and tag via the \code{docker_img} argument. If not provided, \code{gatingset_to_flowjo} will
43
-search for the correct default image corresponding to your \code{cytolib} version.
32
+\code{docker pull public.ecr.aws/x4k5d9i7/cytoverse/gs-to-wsp:latest}
44 33
 }
45 34
 \examples{
46 35
 \dontrun{