Merge pull request #3945 from vgteam/fix-ubuntu-pybind11

Account for Ubuntu 22.04's odd pybind11 install

Makefile

@@ -671,9 +671,10 @@ $(LIB_DIR)/libtabixpp.a: $(LIB_DIR)/libhts.a $(TABIXPP_DIR)/*.cpp $(TABIXPP_DIR)
 # -march=native, which would conflict with the -march that comes in through
 # CXXFLAGS from the vg Dockerfile.
 # We also need to use the magic path hint to let CMake find Mac OpenMP.
+# We need to use /usr first for CMake search or Ubuntu 22.04 will decide pybind11 is installed in / when actually it is only fully installed in /usr.
 $(LIB_DIR)/libvcflib.a: $(LIB_DIR)/libhts.a $(LIB_DIR)/libtabixpp.a $(VCFLIB_DIR)/src/*.cpp $(VCFLIB_DIR)/src/*.hpp $(VCFLIB_DIR)/contrib/*/*.cpp $(VCFLIB_DIR)/contrib/*/*.h
 	+rm -f $(VCFLIB_DIR)/contrib/WFA2-lib/VERSION
-	+. ./source_me.sh && cd $(VCFLIB_DIR) && rm -Rf build && mkdir build && cd build && PKG_CONFIG_PATH="$(CWD)/$(LIB_DIR)/pkgconfig:$(PKG_CONFIG_PATH)" cmake -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DZIG=OFF -DCMAKE_C_FLAGS="$(CFLAGS)" -DCMAKE_CXX_FLAGS="$(CXXFLAGS) ${CPPFLAGS}" -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_PREFIX_PATH="$(OMP_PREFIXES)" .. && cmake --build .
+	+. ./source_me.sh && cd $(VCFLIB_DIR) && rm -Rf build && mkdir build && cd build && PKG_CONFIG_PATH="$(CWD)/$(LIB_DIR)/pkgconfig:$(PKG_CONFIG_PATH)" cmake -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DZIG=OFF -DCMAKE_C_FLAGS="$(CFLAGS)" -DCMAKE_CXX_FLAGS="$(CXXFLAGS) ${CPPFLAGS}" -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_PREFIX_PATH="/usr;$(OMP_PREFIXES)" .. && cmake --build .
 	+cp $(VCFLIB_DIR)/contrib/filevercmp/*.h* $(INC_DIR)
 	+cp $(VCFLIB_DIR)/contrib/fastahack/*.h* $(INC_DIR)
 	+cp $(VCFLIB_DIR)/contrib/smithwaterman/*.h* $(INC_DIR)