Add clearer logging to seurat wrapper code

Author: bbimber

jbrowse/src/org/labkey/jbrowse/model/JsonFile.java

@@ -836,6 +836,9 @@ else if (TRACK_TYPES.gff.getFileType().isType(finalLocation) || TRACK_TYPES.gtf.
                 File exe = JBrowseManager.get().getJbrowseCli();
                 SimpleScriptWrapper wrapper = new SimpleScriptWrapper(log);
                 wrapper.setWorkingDir(targetFile.getParentFile());
+
+                //TODO: eventually remove this. see: https://github.com/GMOD/jbrowse-components/issues/2354#issuecomment-926320747
+                wrapper.addToEnvironment("DEBUG", "*");
                 wrapper.execute(Arrays.asList(exe.getPath(), "text-index", "--force", "--quiet", "--attributes", StringUtils.join(attributes, ","), "--file", targetFile.getPath()));
                 if (!ixx.exists())
                 {

singlecell/resources/chunks/Functions.R

@@ -9,15 +9,16 @@ bindArgs <- function(fun, seuratObj, allowableArgNames = NULL, disallowedArgName
         }
         else if (!is.null(allowableArgNames)) {
             if ((name %in% allowableArgNames) && exists(name)) {
+                print(paste0('Binding argument: ', name, ': ', get(name)))
                 boundArgs[[name]] <- get(name)
             }
         }
         else if (exists(name)) {
+            print(paste0('Binding argument: ', name, ': ', get(name)))
             boundArgs[[name]] <- get(name)
         }
     }
 
-    print(paste0('Binding arguments: ', paste0(names(boundArgs), collapse = ',')))
     formals(fun)[names(boundArgs)] <- boundArgs
 
     fun