Added a couple warnings for situations that could cause the tmp-dir t…

…o not be executable, to help troubleshooting if that causes issues.

src/main/java/org/broadinstitute/hellbender/cmdline/CommandLineProgram.java

@@ -25,6 +25,7 @@
 import org.broadinstitute.hellbender.utils.io.IOUtils;
 import org.broadinstitute.hellbender.utils.runtime.RuntimeUtils;
 
+import java.io.File;
 import java.io.IOException;
 import java.net.InetAddress;
 import java.nio.file.*;
@@ -167,6 +168,33 @@ public Object instanceMainPostParseArgs() {
         final Path p = tmpDir.toPath();
         try {
             p.getFileSystem().provider().checkAccess(p, AccessMode.READ, AccessMode.WRITE);
+
+            // Warn if there's anything that prevents execution in the tmp dir because some tools need that
+            // Write an empty file to the tempdir
+            final Path tempFilePath = Files.createTempFile(p, "gatk_exec_test", null);
+            final File tempFile = tempFilePath.toFile();
+            tempFile.deleteOnExit();
+            // Add execute permissions
+            if(!tempFile.setExecutable(true, false)){
+                logger.warn(
+                    "Cannot create executable files within the configured temporary directory. It is possible " +
+                        "this user does not have the proper permissions to execute files within this directory. " +
+                        "This can cause issues for some GATK tools. You can specify a different directory using " +
+                        "--tmp-dir"
+                );
+            }
+            // Now check if the file can be executed
+            else if(!tempFile.canExecute()) {
+                logger.warn(
+                    "User has permissions to create executable files within the configured temporary directory, " +
+                        "but cannot execute those files. It is possible the directory has been mounted using the " +
+                        "'noexec' flag. This can cause issues for some GATK tools. You can specify a different " +
+                        "directory using --tmp-dir"
+                );
+            }
+
+
+
             System.setProperty("java.io.tmpdir", IOUtils.getAbsolutePathWithoutFileProtocol(p));
         } catch (final AccessDeniedException | NoSuchFileException e) {
             // TODO: it may be that the program does not need a tmp dir