Resolve paragraph executables within PATH

Author: bbimber

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

@@ -289,7 +289,7 @@ protected boolean isThrowNonZeroExits()
         return _throwNonZeroExits;
     }
 
-    protected static File resolveFileInPath(String exe, @Nullable String packageName, boolean throwIfNotFound)
+    public static File resolveFileInPath(String exe, @Nullable String packageName, boolean throwIfNotFound)
     {
         File fn;
         String path;

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

@@ -12,6 +12,7 @@
 import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;
 import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
 import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor;
+import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper;
 import org.labkey.api.sequenceanalysis.run.SimpleScriptWrapper;
 import org.labkey.api.util.FileUtil;
 import org.labkey.sequenceanalysis.SequenceAnalysisModule;
@@ -109,7 +110,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                 //    TNPRC-IB18  ../IB18.cram 29.77   150
 
                 List<String> paragraphArgs = new ArrayList<>();
-                paragraphArgs.add("multigrmpy.py");
+                paragraphArgs.add(AbstractCommandWrapper.resolveFileInPath("multigrmpy.py", null, true).getPath());
                 paragraphArgs.add("--verbose");
 
                 File paragraphOut = new File(ctx.getWorkingDirectory(), FileUtil.getBaseName(so.getFile()) + ".paragraph.txt");