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

run_workflow_phaeoexplorer.py

@@ -987,7 +987,7 @@ if __name__ == "__main__":
             logging.info("Input organism %s: 2 species detected in input dictionary" % k)
 
             # Set workflow path (2 organisms)
-            workflow_path = os.path.join(os.path.abspath(script_dir), "workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v3.ga")
+            workflow_path = os.path.join(os.path.abspath(script_dir), "workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v2.ga")
 
             # Instance object required variables
             instance_url, email, password = None, None, None
@@ -1084,7 +1084,6 @@ if __name__ == "__main__":
             
             # Look for empty parameters values, throw a critical error if a parameter value is invalid
             for param_name, param_value in org2_parameters_dict.items():
-                logging.info("Parameters for organism 1 (%s)" % org2_full_name)
                 if param_value is None or param_value == "":
                     logging.critical("Empty parameter found for organism {0} (parameter: {1}, parameter value: {2})".format(org2_full_name, param_name, param_value))
                     sys.exit()