Release 2.0

• Modification du type de données à la racine du fichier input.yml (liste au lieu d'un dict, le name est ajouté comme item supplémentaire au dictionnaire de chaque espèce sp_dict)
• ajustement de la fonction parse_input() pour tenir compte de la modif précédente
• ajustement du fichier input citrus exemple
• simplification de la fonction get_gspecies_string_from_sp_dict()
• ajout de la date au nom du fichier gff
• fix verbosity arg
• fix banner
• suppression des replace() sur full_name et species_folder_name car genus, species, strain, sex sont "nettoyés" en amont avec la fonction clean_string()

examples/citrus_sinensis.yml

 # Input file for the automated creation GGA docker stacks
 # The file consists in a "list" of species for which the script will have to create these stacks/load data into galaxy/run workflows
-# This file is internally turned into a list of dictionaries by the scripts
 
-citrus_sinensis:  # Dummy value to designate the species (isn't used by the script)
+- name: citrus_sinensis
   description:
   # Species description, leave blank if unknown or you don't want it to be used
   # These parameters are used to set up the various urls and adresses in different containers
@@ -13,11 +12,8 @@ citrus_sinensis:  # Dummy value to designate the species (isn't used by the scri
     strain: ""
     common_name: ""
     origin: ""
-  # the sex and strain, the script will look for files containing the genus, species, sex and strain of the species)
-  # If no file corresponding to the description is found, this path will be considered empty and the script will
-  # proceed to the next step (create the directory tree for the GGA docker stack)
   data:
-  # Sequence of paths to the different datasets to copy and import into the galaxy container (as a shared library)
+  # Paths to the different datasets to copy and import into the galaxy container (as a shared library)
   # Must be absolute paths to the dataset
     genome_path: "/path/to/repo/examples/src_data/genome/v1.0/Citrus_sinensis-scaffold00001.fasta" # Mandatory!
     transcripts_path: "/path/to/repo/examples/src_data/annotation/v1.0/Citrus_sinensis-orange1.1g015632m.g.fasta"  # Mandatory!
@@ -35,8 +31,8 @@ citrus_sinensis:  # Dummy value to designate the species (isn't used by the scri
     ogs_version: "1.0"
     performed_by: ""
   services:
-  # Describe what optional services to deploy for the stack
-  # By default, only tripal, tripaldb and galaxy services will be deployed
+  # List the optional services to be deploy in the stack
+  # By default, only tripal, tripaldb, galaxy, jbrowse and elasticsearch services will be deployed
     blast: "False"
     wiki: "False"
     apollo: "False"
\ No newline at end of file