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

README.md

@@ -74,8 +74,8 @@ $ python3 /path/to/repo/gga_load_data.py input_file.yml -c/--config config_file
 - Run a workflow in galaxy: 
  
 ```bash
-$ python3 /path/to/repo/gga_load_data.py input_file.yml -c/--config config_file --workflow /path/to/workflow.ga [-v/--verbose] [OPTIONS]
-		--workflow $WORKFLOW (Path to the workflow to run in galaxy. A couple of preset workflows are available in the "workflows" folder of the repository)
+$ python3 /path/to/repo/gga_load_data.py input_file.yml -c/--config config_file --workflow workflow_type [-v/--verbose] [OPTIONS]
+		--workflow (Valid options: "chado_load_fasta_gff_jbrowse", "blast", "intepro", a couple of preset workflows are available in the workflows_phaeoexplorer directory in this repository)
 		--main-directory $PATH (Path where to access stacks; default=current directory)
 ```