# HG changeset patch
# User yating-l
# Date 1507925943 14400
# Node ID 2191bd0798a964ad449a0c97faa6e01a0c033e26
# Parent  f5fbe894af85e14cad903c9fbe535b335d8b1c26
planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty

diff -r f5fbe894af85 -r 2191bd0798a9 apollo/ApolloInstance.py
--- a/apollo/ApolloInstance.py	Fri Oct 13 16:00:38 2017 -0400
+++ b/apollo/ApolloInstance.py	Fri Oct 13 16:19:03 2017 -0400
@@ -13,9 +13,11 @@
 
     def createApolloUser(self, apollo_user, admin=None):
         p = subtools.arrow_create_user(apollo_user.user_email, apollo_user.firstname, apollo_user.lastname, apollo_user.password, admin) 
-        user_info = json.loads(p)
-        user_id = user_info.get('userId')
-        if not user_id:
+        print p
+        if p:
+            user_info = json.loads(p)
+            user_id = user_info.get('userId')
+        if not p or not user_id:
             self.logger.debug("Cannot create new user: %s; The user may already exist", apollo_user.user_email)
             user_id = subtools.arrow_get_users(apollo_user.user_email)
         self.logger.debug("Got user_id for new or existing user: user_id = %s", str(user_id))
diff -r f5fbe894af85 -r 2191bd0798a9 jbrowseArchiveCreator.xml
--- a/jbrowseArchiveCreator.xml	Fri Oct 13 16:00:38 2017 -0400
+++ b/jbrowseArchiveCreator.xml	Fri Oct 13 16:19:03 2017 -0400
@@ -34,9 +34,10 @@
 ## Ask the user to enter the genome name
 #silent $data_parameter_dict.update({"genome_name": str($genome_name)})
 #silent $data_parameter_dict.update({"apollo_host": str($apollo_host)})
-if $apollo_users_settings.apollo_users_selector == "yes":
+#if $apollo_users_settings.apollo_users_selector == "yes":
     #set apollo_user = {"firstname": str($apollo_users_settings.firstname), "lastname": str($apollo_users_settings.lastname), "password": str($apollo_users_settings.password), "user_email": str($apollo_users_settings.user_email)}
     $data_parameter_dict.update({"apollo_user": $apollo_user})
+#end if 
 
 ## Function to retrieve the data of the inputs
 #def prepare_json($datatype, $input_to_prepare, $order_index, $extra_data_dict={})
diff -r f5fbe894af85 -r 2191bd0798a9 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Oct 13 16:00:38 2017 -0400
+++ b/tool_dependencies.xml	Fri Oct 13 16:19:03 2017 -0400
@@ -91,6 +91,7 @@
                 </action>
                 <action type="set_environment">
                     <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/apollo</environment_variable>
+                    <environment_variable action="append_to" name="PATH">$INSTALL_DIR/apollo</environment_variable>
                 </action>
             </actions>
         </install>