diff --git a/CMakeLists.txt b/CMakeLists.txt
index 99dc03547dd..0771ac6261e 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -507,6 +507,14 @@ else ()
   set (tgt_file_ext "-shared")
 endif ()
 
+#-----------------------------------------------------------------------------
+# perl is used in some optional src and tests, check availability
+find_package (Perl)
+if (PERL_FOUND)
+  set (H5_PERL_FOUND YES)
+endif ()
+#-----------------------------------------------------------------------------
+
 #-----------------------------------------------------------------------------
 # Option to Build Static executables
 #-----------------------------------------------------------------------------
diff --git a/doxygen/Doxyfile.in b/doxygen/Doxyfile.in
index 24fc4ba12e0..2395d6c1f62 100644
--- a/doxygen/Doxyfile.in
+++ b/doxygen/Doxyfile.in
@@ -263,6 +263,7 @@ TAB_SIZE               = 4
 
 ALIASES                =
 
+@INCLUDE_PATH          = @DOXYGEN_INCLUDE_ALIASES_PATH@
 @INCLUDE               = @DOXYGEN_INCLUDE_ALIASES@
 
 # Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 06b0c8c79e6..a07122df357 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -991,8 +991,7 @@ set (H5_PUBLIC_GENERATED_HEADERS
 option (HDF5_GENERATE_HEADERS "Rebuild Generated Files" ON)
 if (HDF5_GENERATE_HEADERS)
   set_source_files_properties(${H5_GENERATED_HEADERS} PROPERTIES GENERATED TRUE)
-  find_package (Perl)
-  if (PERL_FOUND)
+  if (H5_PERL_FOUND)
     execute_process (
         COMMAND ${PERL_EXECUTABLE} ${HDF5_SOURCE_DIR}/bin/make_err ${HDF5_SRC_DIR}/H5err.txt OUTPUT_VARIABLE SCRIPT_OUTPUT
     )
@@ -1369,34 +1368,43 @@ endif ()
 if (DOXYGEN_FOUND)
   set (DOXYGEN_PACKAGE ${HDF5_PACKAGE})
   set (DOXYGEN_VERSION_STRING ${HDF5_VERSION_STRING})
-  set (DOXYGEN_INCLUDE_ALIASES ${HDF5_DOXYGEN_DIR}/aliases)
+  set (DOXYGEN_INCLUDE_ALIASES_PATH ${HDF5_DOXYGEN_DIR})
+  set (DOXYGEN_INCLUDE_ALIASES aliases)
+  set (DOXYGEN_VERBATIM_VARS DOXYGEN_INCLUDE_ALIASES)
   set (DOXYGEN_PROJECT_LOGO ${HDF5_DOXYGEN_DIR}/img/HDFG-logo.png)
   set (DOXYGEN_PROJECT_BRIEF "C-API Reference")
-  set (DOXYGEN_INPUT_DIRECTORY ${HDF5_SRC_DIR} ${HDF5_DOXYGEN_DIR}/dox ${HDF5_GENERATED_SOURCE_DIR}/shared)
+  set (DOXYGEN_INPUT_DIRECTORY "${HDF5_SRC_DIR} ${HDF5_DOXYGEN_DIR}/dox ${HDF5_GENERATED_SOURCE_DIR}/shared")
   set (DOXYGEN_OPTIMIZE_OUTPUT_FOR_C YES)
   set (DOXYGEN_MACRO_EXPANSION YES)
   set (DOXYGEN_OUTPUT_DIRECTORY ${HDF5_BINARY_DIR}/hdf5lib_docs)
 
+# This configure and custom target work together
   # Replace variables inside @@ with the current values
-  configure_file(${HDF5_DOXYGEN_DIR}/Doxyfile.in Doxyfile @ONLY)
-
-  doxygen_add_docs(hdf5lib_doc
-#      ${common_SRCS} ${shared_gen_SRCS} ${H5_PUBLIC_HEADERS} ${H5_PRIVATE_HEADERS} ${H5_GENERATED_HEADERS} ${HDF5_DOXYGEN_DIR}/dox
-      ${DOXYGEN_INPUT_DIRECTORY}
-      ALL
-      WORKING_DIRECTORY ${HDF5_SRC_DIR}
-      COMMENT "Generating HDF5 library Source Documentation"
-  )
-  install(
+  configure_file (${HDF5_DOXYGEN_DIR}/Doxyfile.in ${HDF5_BINARY_DIR}/Doxyfile @ONLY)
+  add_custom_target (hdf5lib_doc ALL
+        COMMAND ${DOXYGEN_EXECUTABLE} ${HDF5_BINARY_DIR}/Doxyfile
+        WORKING_DIRECTORY ${HDF5_SRC_DIR}
+        COMMENT "Generating HDF5 library Source API documentation with Doxygen"
+        VERBATIM )
+# This cmake function requires that the non-default doxyfile settings are provided with set (DOXYGEN_xxx) commands
+# In addition the doxyfile aliases @INCLUDE option is not supported and would need to be provided in a set (DOXYGEN_ALIASES) command.
+#  doxygen_add_docs (hdf5lib_doc
+##      ${common_SRCS} ${shared_gen_SRCS} ${H5_PUBLIC_HEADERS} ${H5_PRIVATE_HEADERS} ${H5_GENERATED_HEADERS} ${HDF5_DOXYGEN_DIR}/dox
+#      ${DOXYGEN_INPUT_DIRECTORY}
+#      ALL
+#      WORKING_DIRECTORY ${HDF5_SRC_DIR}
+#      COMMENT "Generating HDF5 library Source Documentation"
+#  )
+  install (
       DIRECTORY ${HDF5_BINARY_DIR}/hdf5lib_docs/html
       DESTINATION ${HDF5_INSTALL_DATA_DIR}
       COMPONENT Documents
   )
 
-  if(NOT TARGET doxygen)
-    add_custom_target(doxygen)
-  endif()
+  if (NOT TARGET doxygen)
+    add_custom_target (doxygen)
+  endif ()
 
-  add_dependencies(doxygen hdf5lib_doc)
+  add_dependencies (doxygen hdf5lib_doc)
 
 endif ()
diff --git a/test/CMakeTests.cmake b/test/CMakeTests.cmake
index 242c9189b00..d3e0788aa42 100644
--- a/test/CMakeTests.cmake
+++ b/test/CMakeTests.cmake
@@ -889,8 +889,7 @@ if (ENABLE_EXTENDED_TESTS)
 
 #-- Adding test for flushrefresh
   file (MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/H5TEST/flushrefresh_test")
-  find_package (Perl)
-  if (PERL_FOUND)
+  if (H5_PERL_FOUND)
     add_test (
         NAME H5TEST-testflushrefresh-clear-objects
         COMMAND ${CMAKE_COMMAND} -E remove flushrefresh.h5
diff --git a/test/ShellTests.cmake b/test/ShellTests.cmake
index 4676184caff..4d23de3ced7 100644
--- a/test/ShellTests.cmake
+++ b/test/ShellTests.cmake
@@ -23,8 +23,7 @@ if (UNIX)
     ##############################################################################
     #  configure scripts to test dir
     ##############################################################################
-    find_package (Perl)
-    if (PERL_FOUND)
+    if (H5_PERL_FOUND)
       configure_file(${HDF5_TEST_SOURCE_DIR}/testflushrefresh.sh.in ${HDF5_TEST_BINARY_DIR}/H5TEST/testflushrefresh.sh @ONLY)
     endif ()
     configure_file(${HDF5_TEST_SOURCE_DIR}/test_usecases.sh.in ${HDF5_TEST_BINARY_DIR}/H5TEST/test_usecases.sh @ONLY)