Merge pull request #304 from BimberLab/24.11_fb_merge

Merge discvr-24.7 to discvr-24.11

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/JobResourceSettings.java

@@ -2,6 +2,7 @@
 
 import org.labkey.api.data.Container;
 
+import java.util.Collection;
 import java.util.List;
 
 /**
@@ -12,4 +13,6 @@ public interface JobResourceSettings
     boolean isAvailable(Container c);
 
     List<ToolParameterDescriptor> getParams();
+
+    Collection<String> getDockerVolumes(Container c);
 }

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/PipelineContext.java

@@ -16,11 +16,11 @@
 package org.labkey.api.sequenceanalysis.pipeline;
 
 import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
 import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.WorkDirectory;
 
 import java.io.File;
+import java.util.Collection;
 
 /**
  * User: bimber
@@ -51,4 +51,6 @@ public interface PipelineContext
      * This is the directory where the source files were located.  In the situation where this is a split job, forceParent=true will return the parent job's sourceDirectory.  This can be important if files are written here prior to split.
      */
     File getSourceDirectory(boolean forceParent);
+
+    Collection<String> getDockerVolumes();
 }

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequencePipelineService.java

@@ -19,13 +19,15 @@
 import htsjdk.samtools.SAMFileHeader;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.Nullable;
+import org.labkey.api.data.Container;
 import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.SequenceOutputFile;
 import org.labkey.api.sequenceanalysis.run.CommandWrapper;
 
 import java.io.File;
 import java.io.IOException;
+import java.util.Collection;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -98,6 +100,8 @@ static public void setInstance(SequencePipelineService instance)
      */
     abstract public String getDockerCommand();
 
+    abstract public Collection<String> getDockerVolumes(Container c);
+
     abstract public List<File> getSequenceJobInputFiles(PipelineJob job);
 
     /**

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

@@ -4,6 +4,7 @@
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
 import org.labkey.api.pipeline.PipelineJobException;
+import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
 import org.labkey.api.sequenceanalysis.pipeline.PipelineOutputTracker;
 import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
 import org.labkey.api.writer.PrintWriters;
@@ -17,12 +18,14 @@
 public class DockerWrapper extends AbstractCommandWrapper
 {
     private final String _containerName;
+    private final PipelineContext _ctx;
     private File _tmpDir = null;
 
-    public DockerWrapper(String containerName, Logger log)
+    public DockerWrapper(String containerName, Logger log, PipelineContext ctx)
     {
         super(log);
         _containerName = containerName;
+        _ctx = ctx;
     }
 
     public void setTmpDir(File tmpDir)
@@ -49,6 +52,7 @@ public void executeWithDocker(List<String> containerArgs, File workDir, Pipeline
             writer.println("sudo $DOCKER run --rm=true \\");
             writer.println("\t-v \"${WD}:/work\" \\");
             writer.println("\t-v \"${HOME}:/homeDir\" \\");
+            _ctx.getDockerVolumes().forEach(ln -> writer.println(ln + " \\"));
             if (_tmpDir != null)
             {
                 writer.println("\t-v \"" + _tmpDir.getPath() + ":/tmp\" \\");