Drop UID from docker

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java

@@ -297,8 +297,6 @@ public void execute(List<File> inputGvcfs, File outputVcf, PipelineOutputTracker
                 {
                     writer.println("\t-v \"${TMPDIR}:/tmp\" \\");
                 }
-                writer.println("\t-u $UID \\");
-                writer.println("\t-e USERID=$UID \\");
 
                 Integer maxRam = SequencePipelineService.get().getMaxRam();
                 if (maxRam != null)

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java

@@ -275,8 +275,6 @@ public void execute(File inputBam, File refFasta, File outputGvcf, boolean retai
                 {
                     writer.println("\t-v \"${TMPDIR}:/tmp\" \\");
                 }
-                writer.println("\t-u $UID \\");
-                writer.println("\t-e USERID=$UID \\");
                 writer.println("\t--entrypoint /bin/bash \\");
                 writer.println("\t-w /work \\");
                 Integer maxRam = SequencePipelineService.get().getMaxRam();

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/NextCladeHandler.java

@@ -185,8 +185,6 @@ public static File runNextClade(File consensusFasta, Logger log, PipelineOutputT
 
             writer.println("\t-v \"${WD}:/work\" \\");
             ctx.getDockerVolumes().forEach(ln -> writer.println(ln + " \\"));
-            writer.println("\t-u $UID \\");
-            writer.println("\t-e USERID=$UID \\");
             writer.println("\t-w /work \\");
             writer.println("\tnextstrain/nextclade:latest \\");
             writer.println("\t/bin/bash -c \"nextclade dataset get --name='sars-cov-2' --output-dir='/work/data/sars-cov-2';nextclade run --input-dataset='/work/data/sars-cov-2' --output-json '/work/" + jsonFile.getName() + "' '" + consensusFasta.getName() + "'\" && rm -Rf /work/data");

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PangolinHandler.java

@@ -309,8 +309,6 @@ private static File runUsingDocker(File outputDir, Logger log, File consensusFas
             String extraArgString = extraArgs == null ? "" : " " + StringUtils.join(extraArgs, " ");
             writer.println("\t-v \"${WD}:/work\" \\");
             ctx.getDockerVolumes().forEach(ln -> writer.println(ln + " \\"));
-            writer.println("\t-u $UID \\");
-            writer.println("\t-e USERID=$UID \\");
             writer.println("\t-w /work \\");
             writer.println("\tghcr.io/bimberlabinternal/pangolin:latest \\");
             writer.println("\tpangolin" + extraArgString + " '/work/" + consensusFasta.getName() + "'");

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

@@ -352,8 +352,6 @@ public static void executeR(SequenceOutputHandler.JobContext ctx, String dockerC
             writer.println("\t-v \"" + tmpDir.getPath() + ":/tmp\" \\");
             ctx.getDockerVolumes().forEach(ln -> writer.println(ln + " \\"));
             writer.println("\t-v \"${HOME}:/homeDir\" \\");
-            writer.println("\t-u $UID \\");
-            writer.println("\t-e USERID=$UID \\");
             writer.println("\t-e TMPDIR=/tmp \\");
             if (dockerHomeDir != null)
             {

singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java

@@ -1328,8 +1328,6 @@ public File generateCellHashingCalls(File citeSeqCountOutDir, File outputDir, St
             writer.println("\t-v \"${WD}:/work\" \\");
             ctx.getDockerVolumes().forEach(ln -> writer.println(ln + " \\"));
             writer.println("\t-v \"${HOME}:/homeDir\" \\");
-            writer.println("\t-u $UID \\");
-            writer.println("\t-e USERID=$UID \\");
             writer.println("\t-w /work \\");
             writer.println("\tghcr.io/bimberlab/cellhashr:latest \\");
             writer.println("\tRscript --vanilla " + localRScript.getName());

singlecell/src/org/labkey/singlecell/run/NimbleHelper.java

@@ -608,10 +608,8 @@ private static boolean runUsingDocker(List<String> nimbleArgs, PipelineStepOutpu
             ctx.getDockerVolumes().forEach(ln -> writer.println(ln + " \\"));
             writer.println("\t-v \"${WD}:/work\" \\");
             writer.println("\t-v \"${HOME}:/homeDir\" \\");
-            writer.println("\t-u $UID \\");
             writer.println("\t-e RUST_BACKTRACE=1 \\");
             writer.println("\t-e TMPDIR=/work/tmpDir \\");
-            writer.println("\t-e USERID=$UID \\");
             writer.println("\t--entrypoint /bin/bash \\");
             writer.println("\t-w /work \\");
             writer.println("\t" + DOCKER_CONTAINER_NAME + " \\");