Set HOME environment variable for CellMembrane docker containers

Author: bbimber

singlecell/api-src/org/labkey/api/singlecell/pipeline/AbstractSingleCellPipelineStep.java

@@ -282,7 +282,7 @@ protected void executeR(SequenceOutputHandler.JobContext ctx, File rmd, String o
             seuratThreads = getProvider().getParameterByName(SEURAT_THREADS).extractValue(ctx.getJob(), getProvider(), getStepIdx(), Integer.class, null);
         }
 
-        executeR(ctx, getDockerContainerName(), outputPrefix, lines, seuratThreads);
+        executeR(ctx, getDockerContainerName(), outputPrefix, lines, seuratThreads, getDockerHomeDir());
 
         handlePossibleFailure(ctx, outputPrefix);
     }
@@ -294,7 +294,7 @@ protected static SeuratToolParameter getSeuratThreadsParam()
         }}, null);
     }
 
-    public static void executeR(SequenceOutputHandler.JobContext ctx, String dockerContainerName, String outputPrefix, List<String> lines, @Nullable Integer seuratThreads) throws PipelineJobException
+    public static void executeR(SequenceOutputHandler.JobContext ctx, String dockerContainerName, String outputPrefix, List<String> lines, @Nullable Integer seuratThreads, @Nullable String dockerHomeDir) throws PipelineJobException
     {
         File localRScript = new File(ctx.getOutputDir(), FileUtil.makeLegalName(outputPrefix + ".R").replaceAll(" ", "_"));
         try (PrintWriter writer = PrintWriters.getPrintWriter(localRScript))
@@ -349,6 +349,10 @@ public static void executeR(SequenceOutputHandler.JobContext ctx, String dockerC
             writer.println("\t-u $UID \\");
             writer.println("\t-e USERID=$UID \\");
             writer.println("\t-e TMPDIR=/tmp \\");
+            if (dockerHomeDir != null)
+            {
+                writer.println("\t-e HOME=" + dockerHomeDir + " \\");
+            }
             writer.println("\t-w /work \\");
             //NOTE: this seems to disrupt packages installed into home
             //writer.println("\t-e HOME=/homeDir \\");
@@ -371,6 +375,11 @@ public static void executeR(SequenceOutputHandler.JobContext ctx, String dockerC
         localBashScript.delete();
     }
 
+    public String getDockerHomeDir()
+    {
+        return null;
+    }
+
     protected void addParameterVariables(SeuratToolParameter pd, List<String> body)
     {
         String val = StringUtils.trimToNull(pd.extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx()));

singlecell/resources/chunks/CommonFilters.R

@@ -149,7 +149,7 @@ for (datasetId in names(seuratObjects)) {
 				seuratObj <- subset(seuratObj, cells = negativeCells, invert = TRUE)
 				print(paste0('After removing cells with negative hashing calls: ', ncol(seuratObj)))
 				if (ncol(seuratObj) != expectedCells) {
-					stop(paste0('The subset for negative hashing cells did not work as expected. Expected cells: ', expectedCells, ', actual: ', ncol(seuratObj))
+					stop(paste0('The subset for negative hashing cells did not work as expected. Expected cells: ', expectedCells, ', actual: ', ncol(seuratObj)))
 				}
 			}
 		}, error = function(e){

singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java

@@ -597,7 +597,7 @@ else if (step.createsSeuratObjects())
             File finalHtml = new File(ctx.getOutputDir(), "finalHtml.html");
             List<String> lines = new ArrayList<>();
             lines.add("rmarkdown::render(output_file = '" + finalHtml.getName() + "', input = '" + finalMarkdownFile.getName() + "', intermediates_dir  = '/work')");
-            AbstractSingleCellPipelineStep.executeR(ctx, AbstractCellMembraneStep.CONTAINER_NAME, "pandoc", lines, null);
+            AbstractSingleCellPipelineStep.executeR(ctx, AbstractCellMembraneStep.CONTAINER_NAME, "pandoc", lines, null, null);
             _resumer.getFileManager().addIntermediateFile(finalMarkdownFile);
             _resumer.getFileManager().addIntermediateFiles(_resumer.getMarkdownsInOrder());
             _resumer.getFileManager().addIntermediateFiles(_resumer.getHtmlFilesInOrder());

singlecell/src/org/labkey/singlecell/pipeline/singlecell/AbstractCellMembraneStep.java

@@ -11,7 +11,7 @@ abstract public class AbstractCellMembraneStep extends AbstractSingleCellPipelin
 {
     public static String CONTAINER_NAME = "ghcr.io/bimberlabinternal/cellmembrane:latest";
 
-    public AbstractCellMembraneStep(PipelineStepProvider provider, PipelineContext ctx)
+    public AbstractCellMembraneStep(PipelineStepProvider<?> provider, PipelineContext ctx)
     {
         super(provider, ctx);
     }
@@ -27,4 +27,11 @@ public String getDockerContainerName()
     {
         return CONTAINER_NAME;
     }
+
+    // NOTE: ExperimentHub and similar packages default to saving data to the user's home dir. Set a directory, to avoid issues when not running the container as root
+    @Override
+    public String getDockerHomeDir()
+    {
+        return "/dockerHomeDir";
+    }
 }