Add --group-add keep-groups to docker

bbimber · bbimber · commit 8157f85e51e3 · 2024-12-02T13:41:49.000-08:00
diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/DockerWrapper.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/DockerWrapper.java
@@ -62,13 +62,14 @@ public void executeWithDocker(List<String> containerArgs, File workDir, Pipeline
             writer.println("WD=`pwd`");
 
             writer.println("DOCKER='" + SequencePipelineService.get().getDockerCommand() + "'");
+            writer.println("$DOCKER pull " + _containerName);
             if (_runPrune)
             {
                 writer.println("$DOCKER image prune -f");
             }
 
-            writer.println("$DOCKER pull " + _containerName);
             writer.println("$DOCKER run --rm=true \\");
+            writer.println("\t--group-add keep-groups \\");
 
             // NOTE: getDockerVolumes() should be refactored to remove the -v and this logic should be updated accordingly:
             File homeDir = new File(System.getProperty("user.home"));

Original file line number	Diff line number	Diff line change
`@@ -62,13 +62,14 @@ public void executeWithDocker(List<String> containerArgs, File workDir, Pipeline`
`62`	`62`	writer.println("WD=`pwd`");
`63`	`63`
`64`	`64`	`writer.println("DOCKER='" + SequencePipelineService.get().getDockerCommand() + "'");`
	`65`	`+ writer.println("$DOCKER pull " + _containerName);`
`65`	`66`	`if (_runPrune)`
`66`	`67`	`{`
`67`	`68`	`writer.println("$DOCKER image prune -f");`
`68`	`69`	`}`
`69`	`70`
`70`		`- writer.println("$DOCKER pull " + _containerName);`
`71`	`71`	`writer.println("$DOCKER run --rm=true \\");`
	`72`	`+ writer.println("\t--group-add keep-groups \\");`
`72`	`73`
`73`	`74`	`// NOTE: getDockerVolumes() should be refactored to remove the -v and this logic should be updated accordingly:`
`74`	`75`	`File homeDir = new File(System.getProperty("user.home"));`