fix typo, renamed files in 'files' dir, fix for jbrowee menu url

gga_init.py

@@ -79,11 +79,15 @@ class DeploySpeciesStack(speciesData.SpeciesData):
         # Create nginx dirs and write/re-write nginx conf
         make_dirs(dir_paths_li=["./nginx", "./nginx/conf"])
         try:
-            with open(os.path.abspath("./nginx/conf/default.conf"), 'w') as conf:
-                conf.write("server {\n\tlisten 80;\n\tserver_name ~.;\n\tlocation /download/ {\n\t\talias /project_data/; \n\t\tautoindex on;\n\t}\n}")  # The species nginx conf
-        except OSError as exc:
-            logging.critical("Cannot write NginX conf file")
-            sys.exit(exc)
+            shutil.copy(os.path.join(self.script_dir, "files/nginx_download.conf"), os.path.abspath("./nginx/conf/default.conf"))
+        except Exception as exc:
+            logging.critical("Could not copy nginx configuration file for %s" % self.full_name)
+            logging.critical(exc)            
+        #     with open(os.path.abspath("./nginx/conf/default.conf"), 'w') as conf:
+        #         conf.write("server {\n\tlisten 80;\n\tserver_name ~.;\n\tlocation /download/ {\n\t\talias /project_data/; \n\t\tautoindex on;\n\t}\n}")  # The species nginx conf
+        # except OSError as exc:
+        #     logging.critical("Cannot write NginX conf file")
+        #     sys.exit(exc)
 
         # Return to main directory
         os.chdir(self.main_dir)
@@ -128,7 +132,7 @@ class DeploySpeciesStack(speciesData.SpeciesData):
             gspecies_compose_file.write(gspecies_compose_output)
 
 
-        galaxy_nginx_conf_template = env.get_template("galaxy_nginx_conf.j2")
+        galaxy_nginx_conf_template = env.get_template("galaxy_nginx.conf.j2")
         galaxy_nginx_conf_output = galaxy_nginx_conf_template.render(render_vars)
         with open(os.path.join(self.main_dir, "galaxy_nginx.conf"), "w") as galaxy_nginx_conf_file:
             logging.debug("Writing the galaxy_nginx.conf file for %s" % self.genus_species)

run_workflow_phaeoexplorer.py

@@ -493,7 +493,7 @@ class RunWorkflow(speciesData.SpeciesData):
             # as runtime values, using runtime parameters makes the tool throw an internal critical error ("replace not found" error)
             # Scratchgmod test: need "http" (or "https"), the hostname (+ port)
             if "menu_url" not in self.config.keys():
-                jbrowse_menu_url = "https://{hostname}/sp/{genus_sp}/feature/{Genus}/{species}/{id}".format(hostname=self.config["hostname"], genus_sp=self.genus_species, Genus=self.genus_uppercase, species=self.species, id="{id}")
+                jbrowse_menu_url = "https://{hostname}/sp/{genus_sp}/feature/{Genus}/{species}/mRNA/{id}".format(hostname=self.config["hostname"], genus_sp=self.genus_species, Genus=self.genus_uppercase, species=self.species, id="{id}")
             else:
                 jbrowse_menu_url = self.config["menu_url"]
             if workflow_name == "Jbrowse":