Migrate from ProcessBuilder to LabKeyProcessBuilder

Author: labkey-jeckels

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceRemoteIntegrationTests.java

@@ -16,6 +16,7 @@
 import org.labkey.api.pipeline.WorkDirectory;
 import org.labkey.api.reader.Readers;
 import org.labkey.api.util.FileUtil;
+import org.labkey.api.util.LabKeyProcessBuilder;
 import org.labkey.api.writer.PrintWriters;
 import org.labkey.sequenceanalysis.pipeline.AlignmentInitTask;
 import org.labkey.sequenceanalysis.pipeline.PrepareAlignerIndexesTask;
@@ -212,7 +213,7 @@ protected void executeJobRemote(File workDir, @Nullable File jobJson) throws IOE
             args.add(jobJson.toURI().toString());
         }
 
-        ProcessBuilder pb = new ProcessBuilder(args);
+        LabKeyProcessBuilder pb = new LabKeyProcessBuilder(args);
         pb.directory(workDir);
 
         _log.info("Executing job in '{}': {}", pb.directory().getAbsolutePath(), String.join(" ", pb.command()));

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java

@@ -33,6 +33,7 @@
 import org.labkey.api.util.Compress;
 import org.labkey.api.util.FileType;
 import org.labkey.api.util.FileUtil;
+import org.labkey.api.util.LabKeyProcessBuilder;
 import org.labkey.api.util.Path;
 import org.labkey.api.util.StringUtilsLabKey;
 import org.labkey.sequenceanalysis.SequenceAnalysisModule;
@@ -139,7 +140,7 @@ private void runForFile(File f)
 
             _logger.info("running fastqc:");
             _logger.info(StringUtils.join(params, " "));
-            ProcessBuilder pb = new ProcessBuilder(params);
+            LabKeyProcessBuilder pb = new LabKeyProcessBuilder(params);
             pb.redirectErrorStream(true);
             pb.directory(f.getParentFile());