Don't require python to just instantiate tool classes. (#8128)

* Don't require python to just instantiate tool classes.

src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNScoreVariants.java

@@ -205,9 +205,7 @@ public class CNNScoreVariants extends TwoPassVariantWalker {
     @Argument(fullName = "python-profile", shortName = "python-profile", doc = "Run the tool with the Python CProfiler on and write results to this file.", optional = true)
     private File pythonProfileResults;
 
-    // Create the Python executor. This doesn't actually start the Python process, but verifies that
-    // the requestedPython executable exists and can be located.
-    final StreamingPythonScriptExecutor<String> pythonExecutor = new StreamingPythonScriptExecutor<>(true);
+    private StreamingPythonScriptExecutor<String> pythonExecutor;
 
     private List<String> batchList = new ArrayList<>(inferenceBatchSize);
 
@@ -284,6 +282,10 @@ public void onTraversalStart() {
             }
         }
 
+        // Create the Python executor. This doesn't actually start the Python process, but verifies that
+        // the requestedPython executable exists and can be located.
+        pythonExecutor = new StreamingPythonScriptExecutor<>(true);
+
         final VCFHeader inputHeader = getHeaderForVariants();
         if (inputHeader.getGenotypeSamples().size() > 1) {
             logger.warn("CNNScoreVariants is a single sample tool but the input VCF has more than 1 sample.");

src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNVariantTrain.java

@@ -129,17 +129,19 @@ public class CNNVariantTrain extends CommandLineProgram {
     @Argument(fullName = "annotation-set", shortName = "annotation-set", doc = "Which set of annotations to use.", optional = true)
     private String annotationSet = "best_practices";
 
-    // Start the Python executor. This does not actually start the Python process, but fails if python can't be located
-    final PythonScriptExecutor pythonExecutor = new PythonScriptExecutor(true);
+    private PythonScriptExecutor pythonExecutor;
 
 
     @Override
     protected void onStartup() {
         PythonScriptExecutor.checkPythonEnvironmentForPackage("vqsr_cnn");
+        // Start the Python executor. This does not actually start the Python process, but fails if python can't be located
+        pythonExecutor = new PythonScriptExecutor(true);
     }
 
     @Override
     protected Object doWork() {
+
         final Resource pythonScriptResource = new Resource("training.py", CNNVariantTrain.class);
         List<String> arguments = new ArrayList<>(Arrays.asList(
                 "--data_dir", inputTensorDir,

src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNVariantWriteTensors.java

@@ -117,16 +117,19 @@ public class CNNVariantWriteTensors extends CommandLineProgram {
     @Argument(fullName = "max-tensors", shortName = "max-tensors", doc = "Maximum number of tensors to write.", optional = true, minValue = 0)
     private int maxTensors = 1000000;
 
-    // Start the Python executor. This does not actually start the Python process, but fails if python can't be located
-    final PythonScriptExecutor pythonExecutor = new PythonScriptExecutor(true);
+    private PythonScriptExecutor pythonExecutor;
 
     @Override
     protected void onStartup() {
         PythonScriptExecutor.checkPythonEnvironmentForPackage("vqsr_cnn");
+
+        // Start the Python executor. This does not actually start the Python process, but fails if python can't be located
+        pythonExecutor = new PythonScriptExecutor(true);
     }
 
     @Override
     protected Object doWork() {
+
         final Resource pythonScriptResource = new Resource("training.py", CNNVariantWriteTensors.class);
         List<String> arguments = new ArrayList<>(Arrays.asList(
                 "--reference_fasta", reference,