Release 2.0 (merge dev to master)

General

• Reorganize repository
• Fix verbosity mode
• Fix logs details
• Update README.md
• Update the "help" option in the scripts
• Update examples
• Factorize and optimize code
• Create file constants.py containing the constant variables

Input organisms.yml file

• Change root structure (a list instead of a dictionary, the name parameter is added to the species dictionary sp_dict)
• Add parameter main_species. Useful when there are multiple strains for the same species: set to yes to define the strain used as home for JBrowse
• Parameters species, genus, strain, sex, common will be sanitized (removing " ", "-", "(", ")", "'")
• Add jinja2 template

Input config file

• Change root structure (one-level dictionary)
• Add parameters authelia_secrets_env_path and authelia_db_postgres_password required for Authelia
• Change the name of some parameters (galaxy_persist_data, tripal_banner_path, jbrowse_menu_url)
• Remove unused apollo parameters (webapollo_user, webapollo_password)

Step "init"

• Update templates files
• Fix the copy of the specified banner
• Write galaxy_nginx.conf only if needed

Step "get data"

• Prefix data filenames with g_species_s
• Add the last modification date of the source file to the gff filename

Step "load data"

• Use Bioblend function upload_from_galaxy_fs() instead of upload_from_local() (to enable symlink, instead of copy)

Step "run workflow Phaeoexplorer"

• Development of a workflow loading fasta and gff files to Chado, Tripal and JBrowse, for one or two organisms of the same species

gga_init.py

@@ -62,11 +62,10 @@ class DeploySpeciesStack(speciesData.SpeciesData):
         # use the default banner instead
         if "banner_path" in self.config.keys():
             if not config["banner_path"] == "" and os.path.isfile(os.path.abspath(config["banner_path"])):
-                banner_dest_path = os.path.abspath("./banner.png")
-                logging.info("Custom banner path: %s" % self.config["banner_path"])
-                # if os.path.samefile(os.path.abspath(config["banner_path"]), banner_dest_path):
-                    # shutil.copy(os.path.abspath(self.config["banner_path"]), banner_dest_path)
-                shutil.copy(os.path.abspath(self.config["banner_path"]), banner_dest_path)
+                banner_dest_path = os.path.join(self.species_dir, os.path.abspath("banner.png"))
+                if not os.path.samefile(os.path.abspath(config["banner_path"]),banner_dest_path):
+                    os.symlink(os.path.abspath(self.config["banner_path"]), banner_dest_path)
+                    logging.info("Custom banner added: symlink from %s" % self.config["banner_path"])
             else:
                 logging.debug("Using default banner for Tripal pages")
                 self.config.pop("banner_path", None)