Try it like this...

.travis.yml

 # Travis-CI Build for libgit2
 # see travis-ci.org for details
+
+# As CMake is not officially supported we use erlang VMs
 language: c
 
 compiler:
@@ -26,8 +28,8 @@ script:
  - mkdir _build
  - cd _build
  - cmake .. -DCMAKE_INSTALL_PREFIX=../_install $OPTIONS
- - make submodules all
- - ./libgit2_clar
+ - cmake --build . --target install
+ - ctest -V .
 
 # Run Tests
 after_script:

CMakeLists.txt

@@ -231,13 +231,6 @@ INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/libgit2.pc DESTINATION ${LIB_INSTALL_D
 INSTALL(DIRECTORY include/git2 DESTINATION ${INCLUDE_INSTALL_DIR} )
 INSTALL(FILES include/git2.h DESTINATION ${INCLUDE_INSTALL_DIR} )
 
-
-ADD_CUSTOM_TARGET(
-	submodules
-	COMMAND git submodule update --init tests-clar/clar
-	WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-)
-
 # Tests
 IF (BUILD_CLAR)
 	FIND_PACKAGE(PythonInterp REQUIRED)
@@ -254,6 +247,11 @@ IF (BUILD_CLAR)
 	SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-missing-prototypes")
 
 	ADD_CUSTOM_COMMAND(
+		OUTPUT ${CLAR_PATH}/clar/clar.c
+		COMMAND git submodule update --init tests-clar/clar
+	)
+
+	ADD_CUSTOM_COMMAND(
 		OUTPUT ${CLAR_PATH}/clar.suite
 		COMMAND ${PYTHON_EXECUTABLE} clar/generate.py .
 		DEPENDS ${SRC_TEST}