Release_2.0 next

General

• Move constants to file constants.py
• Set default config file in scripts.
• Update description of scripts in main.
• Update README.md

Input config file

• Change config root to dict and update parse_config().
• Change some config parameters name (galaxy_persist_data, tripal_banner_path, jbrowse_menu_url), update example config file and compose templates.
• Remove apollo config variables (webapollo_user, webapollo_password) in config file and in gspecies compose template, because apollo service not deployed here.

Utilities.py

• Factorize parse_input() et parse_config().
• Get input yml keys from constants (update organisms.yml.j2 and add create_org_param_dict_from_constants())

gspecies_compose.yml

• set ENABLE_WIKI and ENABLE_APOLLO to 0 in gspecies compose template
• fix ENABLE_BLAST value in gspecies compose template

gga_get_data.py

• Remove useless variable datasets_to_get

gga_init.py

• replace subprocess.call() with subprocess.run(). Factorize run_command() and run_docker_stack_deploy()
• fix banner copy

gga_init.py

@@ -64,7 +64,7 @@ class DeploySpeciesStack(speciesData.SpeciesData):
         if constants.CONF_TRIPAL_BANNER_PATH in self.config.keys():
             if not config[constants.CONF_TRIPAL_BANNER_PATH] == "" and os.path.isfile(os.path.abspath(config[constants.CONF_TRIPAL_BANNER_PATH])):
                 banner_dest_path = os.path.join(self.species_dir, os.path.abspath("banner.png"))
-                if not os.path.isfile(banner_dest_path) or not os.path.samefile(os.path.abspath(config[constants.CONF_TRIPAL_BANNER_PATH]),banner_dest_path):
+                if not os.path.isfile(banner_dest_path) or not os.path.islink(banner_dest_path) or not os.path.samefile(os.path.abspath(config[constants.CONF_TRIPAL_BANNER_PATH]),banner_dest_path):
                     os.symlink(os.path.abspath(self.config[constants.CONF_TRIPAL_BANNER_PATH]), banner_dest_path)
                     logging.info("Custom banner added: symlink from %s" % self.config[constants.CONF_TRIPAL_BANNER_PATH])
             else:
@@ -134,7 +134,7 @@ class DeploySpeciesStack(speciesData.SpeciesData):
                 galaxy_nginx_conf_file.truncate(0)
                 galaxy_nginx_conf_file.write(galaxy_nginx_conf_output)
         else:
-            logging.debug("galaxy_nginx.conf alredy exists")
+            logging.debug("galaxy_nginx.conf already exists")
 
         # Create the volumes (directory) of the species docker-compose file
         create_mounts(working_dir=".", main_dir=self.main_dir)