diff --git a/doc/conf.py b/doc/conf.py
index f1c120b5..e76bf8c9 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -33,7 +33,9 @@ on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
 if on_rtd:
   sys.path.append("../GPy")
   os.system("pwd")
-  os.system("sphinx-apidoc -f -o . ../GPy")
+  os.system("cd ..")
+  os.system("sphinx-apidoc -f -o ./docs ./GPy")
+  os.system("cd ./docs")
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']