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bbimberbbimber
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Switch ParagraphStep to use docker
1 parent 82ecaa8 commit 881d11d

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+123
-9
lines changed

2 files changed

+123
-9
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‎SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/DockerWrapper.java‎

Lines changed: 107 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,107 @@
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package org.labkey.api.sequenceanalysis.run;
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import org.apache.commons.io.FileUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.logging.log4j.Logger;
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import org.labkey.api.pipeline.PipelineJobException;
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import org.labkey.api.sequenceanalysis.pipeline.PipelineOutputTracker;
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import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
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import org.labkey.api.writer.PrintWriters;
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import java.io.File;
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import java.io.IOException;
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import java.io.PrintWriter;
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import java.util.List;
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public class DockerWrapper extends AbstractCommandWrapper
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{
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private final String _containerName;
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private File _tmpDir = null;
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public DockerWrapper(String containerName, Logger log)
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{
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super(log);
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_containerName = containerName;
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}
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public void setTmpDir(File tmpDir)
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{
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_tmpDir = tmpDir;
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}
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public void execute(List<String> containerArgs, File workDir, PipelineOutputTracker tracker) throws PipelineJobException
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{
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File localBashScript = new File(workDir, "docker.sh");
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File dockerBashScript = new File(workDir, "dockerRun.sh");
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tracker.addIntermediateFile(localBashScript);
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tracker.addIntermediateFile(dockerBashScript);
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setWorkingDir(workDir);
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try (PrintWriter writer = PrintWriters.getPrintWriter(localBashScript); PrintWriter dockerWriter = PrintWriters.getPrintWriter(dockerBashScript))
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{
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writer.println("#!/bin/bash");
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writer.println("set -x");
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writer.println("WD=`pwd`");
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writer.println("HOME=`echo ~/`");
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writer.println("DOCKER='" + SequencePipelineService.get().getDockerCommand() + "'");
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writer.println("sudo $DOCKER pull " + _containerName);
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writer.println("sudo $DOCKER run --rm=true \\");
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writer.println("\t-v \"${WD}:/work\" \\");
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writer.println("\t-v \"${HOME}:/homeDir\" \\");
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if (_tmpDir != null)
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{
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writer.println("\t-v \"" + _tmpDir.getPath() + ":/tmp\" \\");
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}
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writer.println("\t--entrypoint /bin/bash \\");
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writer.println("\t-w /work \\");
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Integer maxRam = SequencePipelineService.get().getMaxRam();
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if (maxRam != null)
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{
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writer.println("\t-e SEQUENCEANALYSIS_MAX_RAM=" + maxRam + " \\");
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writer.println("\t--memory='" + maxRam + "g' \\");
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}
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writer.println("\t" + _containerName + " \\");
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writer.println("\t/work/" + dockerBashScript.getName());
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writer.println("EXIT_CODE=$?");
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writer.println("echo 'Docker run exit code: '$EXIT_CODE");
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writer.println("exit $EXIT_CODE");
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dockerWriter.println("#!/bin/bash");
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dockerWriter.println("set -x");
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dockerWriter.println(StringUtils.join(containerArgs, " "));
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dockerWriter.println("EXIT_CODE=$?");
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dockerWriter.println("echo 'Exit code: '$?");
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dockerWriter.println("exit $EXIT_CODE");
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}
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catch (IOException e)
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{
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throw new PipelineJobException(e);
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}
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}
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public File ensureLocalCopy(File input, File workingDirectory, PipelineOutputTracker output) throws PipelineJobException
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{
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try
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{
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if (workingDirectory.equals(input.getParentFile()))
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{
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return input;
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}
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File local = new File(workingDirectory, input.getName());
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if (!local.exists())
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{
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getLogger().debug("Copying file locally: " + input.getPath());
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FileUtils.copyFile(input, local);
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}
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output.addIntermediateFile(local);
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return local;
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}
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catch (IOException e)
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{
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throw new PipelineJobException(e);
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}
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}
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}

‎SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java‎

Lines changed: 16 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -16,7 +16,7 @@
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import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;
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import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
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import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor;
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import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper;
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import org.labkey.api.sequenceanalysis.run.DockerWrapper;
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import org.labkey.api.sequenceanalysis.run.SimpleScriptWrapper;
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import org.labkey.api.util.FileUtil;
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import org.labkey.api.writer.PrintWriters;
@@ -153,25 +153,32 @@ else if (header.getReadGroups().size() > 1)
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}
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ctx.getFileManager().addIntermediateFile(coverageFile);
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DockerWrapper dockerWrapper = new DockerWrapper("ghcr.io/bimberlabinternal/paragraph:latest", ctx.getLogger());
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List<String> paragraphArgs = new ArrayList<>();
157-
paragraphArgs.add(AbstractCommandWrapper.resolveFileInPath("multigrmpy.py", null, true).getPath());
158+
paragraphArgs.add("/opt/paragraph/bin/multigrmpy.py");
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paragraphArgs.add("--verbose");
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160162
File paragraphOut = new File(ctx.getWorkingDirectory(), FileUtil.getBaseName(so.getFile()) + ".paragraph.txt");
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paragraphArgs.add("-o");
162-
paragraphArgs.add(paragraphOut.getPath());
164+
paragraphArgs.add("/work/" + paragraphOut.getName());
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paragraphArgs.add("-i");
165-
paragraphArgs.add(svVcf.getPath());
167+
dockerWrapper.ensureLocalCopy(svVcf, ctx.getWorkingDirectory(), ctx.getFileManager());
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paragraphArgs.add("/work/" + svVcf.getName());
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167170
paragraphArgs.add("-m");
168-
paragraphArgs.add(coverageFile.getPath());
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paragraphArgs.add("/work/" + coverageFile.getName());
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170173
paragraphArgs.add("-r");
171-
paragraphArgs.add(ctx.getSequenceSupport().getCachedGenome(so.getLibrary_id()).getWorkingFastaFile().getPath());
174+
File genomeFasta = ctx.getSequenceSupport().getCachedGenome(so.getLibrary_id()).getWorkingFastaFile();
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dockerWrapper.ensureLocalCopy(genomeFasta, ctx.getWorkingDirectory(), ctx.getFileManager());
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dockerWrapper.ensureLocalCopy(new File(genomeFasta.getPath() + ".fai"), ctx.getWorkingDirectory(), ctx.getFileManager());
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paragraphArgs.add("/work/" + genomeFasta.getName());
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173179
paragraphArgs.add("--scratch-dir");
174-
paragraphArgs.add(SequencePipelineService.get().getJavaTempDir());
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paragraphArgs.add("/tmp");
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dockerWrapper.setTmpDir(new File(SequencePipelineService.get().getJavaTempDir()));
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176183
if (threads != null)
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{
@@ -180,9 +187,9 @@ else if (header.getReadGroups().size() > 1)
180187
}
181188

182189
paragraphArgs.add("--logfile");
183-
paragraphArgs.add(new File(ctx.getWorkingDirectory(), "paragraph.log").getPath());
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paragraphArgs.add(new File("/work/paragraph.log").getPath());
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185-
new SimpleScriptWrapper(ctx.getLogger()).execute(paragraphArgs);
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dockerWrapper.execute(paragraphArgs, ctx.getWorkingDirectory());
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187194
File genotypes = new File(ctx.getWorkingDirectory(), "genotypes.vcf.gz");
188195
if (!genotypes.exists())

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