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bbimberbbimber
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Drop sudo from docker
1 parent cb7d5e1 commit caaeada

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8 files changed

+16
-16
lines changed

8 files changed

+16
-16
lines changed

‎SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/DockerWrapper.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -48,8 +48,8 @@ public void executeWithDocker(List<String> containerArgs, File workDir, Pipeline
4848
writer.println("WD=`pwd`");
4949
writer.println("HOME=`echo ~/`");
5050
writer.println("DOCKER='" + SequencePipelineService.get().getDockerCommand() + "'");
51-
writer.println("sudo $DOCKER pull " + _containerName);
52-
writer.println("sudo $DOCKER run --rm=true \\");
51+
writer.println("$DOCKER pull " + _containerName);
52+
writer.println("$DOCKER run --rm=true \\");
5353
writer.println("\t-v \"${WD}:/work\" \\");
5454
writer.println("\t-v \"${HOME}:/homeDir\" \\");
5555
_ctx.getDockerVolumes().forEach(ln -> writer.println(ln + " \\"));

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

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -287,8 +287,8 @@ public void execute(List<File> inputGvcfs, File outputVcf, PipelineOutputTracker
287287
writer.println("WD=`pwd`");
288288
writer.println("HOME=`echo ~/`");
289289
writer.println("DOCKER='" + SequencePipelineService.get().getDockerCommand() + "'");
290-
writer.println("sudo $DOCKER pull ghcr.io/dnanexus-rnd/glnexus:" + binVersion);
291-
writer.println("sudo $DOCKER run --rm=true \\");
290+
writer.println("$DOCKER pull ghcr.io/dnanexus-rnd/glnexus:" + binVersion);
291+
writer.println("$DOCKER run --rm=true \\");
292292
writer.println("\t-v \"${WD}:/work\" \\");
293293
writer.println("\t-v \"${HOME}:/homeDir\" \\");
294294
ctx.getDockerVolumes().forEach(ln -> writer.println(ln + " \\"));

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

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -266,8 +266,8 @@ public void execute(File inputBam, File refFasta, File outputGvcf, boolean retai
266266
writer.println("WD=`pwd`");
267267
writer.println("HOME=`echo ~/`");
268268
writer.println("DOCKER='" + SequencePipelineService.get().getDockerCommand() + "'");
269-
writer.println("sudo $DOCKER pull google/deepvariant:" + binVersion);
270-
writer.println("sudo $DOCKER run --rm=true \\");
269+
writer.println("$DOCKER pull google/deepvariant:" + binVersion);
270+
writer.println("$DOCKER run --rm=true \\");
271271
writer.println("\t-v \"${WD}:/work\" \\");
272272
writer.println("\t-v \"${HOME}:/homeDir\" \\");
273273
ctx.getDockerVolumes().forEach(ln -> writer.println(ln + " \\"));

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

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -168,8 +168,8 @@ public static File runNextClade(File consensusFasta, Logger log, PipelineOutputT
168168
writer.println("HOME=`echo ~/`");
169169

170170
writer.println("DOCKER='" + SequencePipelineService.get().getDockerCommand() + "'");
171-
writer.println("sudo $DOCKER pull nextstrain/nextclade:latest");
172-
writer.println("sudo $DOCKER run --rm=true \\");
171+
writer.println("$DOCKER pull nextstrain/nextclade:latest");
172+
writer.println("$DOCKER run --rm=true \\");
173173

174174
if (SequencePipelineService.get().getMaxThreads(log) != null)
175175
{

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

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -291,8 +291,8 @@ private static File runUsingDocker(File outputDir, Logger log, File consensusFas
291291
writer.println("HOME=`echo ~/`");
292292

293293
writer.println("DOCKER='" + SequencePipelineService.get().getDockerCommand() + "'");
294-
writer.println("sudo $DOCKER pull ghcr.io/bimberlabinternal/pangolin:latest");
295-
writer.println("sudo $DOCKER run --rm=true \\");
294+
writer.println("$DOCKER pull ghcr.io/bimberlabinternal/pangolin:latest");
295+
writer.println("$DOCKER run --rm=true \\");
296296

297297
if (SequencePipelineService.get().getMaxThreads(log) != null)
298298
{

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

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -320,8 +320,8 @@ public static void executeR(SequenceOutputHandler.JobContext ctx, String dockerC
320320
writer.println("HOME=`echo ~/`");
321321

322322
writer.println("DOCKER='" + SequencePipelineService.get().getDockerCommand() + "'");
323-
writer.println("sudo $DOCKER pull " + dockerContainerName);
324-
writer.println("sudo $DOCKER run --rm=true \\");
323+
writer.println("$DOCKER pull " + dockerContainerName);
324+
writer.println("$DOCKER run --rm=true \\");
325325

326326
Integer maxThreads = SequencePipelineService.get().getMaxThreads(ctx.getLogger());
327327
if (maxThreads != null)

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

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1311,8 +1311,8 @@ public File generateCellHashingCalls(File citeSeqCountOutDir, File outputDir, St
13111311
writer.println("HOME=`echo ~/`");
13121312

13131313
writer.println("DOCKER='" + SequencePipelineService.get().getDockerCommand() + "'");
1314-
writer.println("sudo $DOCKER pull ghcr.io/bimberlab/cellhashr:latest");
1315-
writer.println("sudo $DOCKER run --rm=true \\");
1314+
writer.println("$DOCKER pull ghcr.io/bimberlab/cellhashr:latest");
1315+
writer.println("$DOCKER run --rm=true \\");
13161316
if (SequencePipelineService.get().getMaxRam() != null)
13171317
{
13181318
writer.println("\t--memory=" + SequencePipelineService.get().getMaxRam() + "g \\");

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

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -594,8 +594,8 @@ private static boolean runUsingDocker(List<String> nimbleArgs, PipelineStepOutpu
594594
writer.println("HOME=`echo ~/`");
595595

596596
writer.println("DOCKER='" + SequencePipelineService.get().getDockerCommand() + "'");
597-
writer.println("sudo $DOCKER pull " + DOCKER_CONTAINER_NAME);
598-
writer.println("sudo $DOCKER run --rm=true \\");
597+
writer.println("$DOCKER pull " + DOCKER_CONTAINER_NAME);
598+
writer.println("$DOCKER run --rm=true \\");
599599

600600
Integer maxRam = SequencePipelineService.get().getMaxRam();
601601
if (maxRam != null)

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