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

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
   # The script requires at least the genus to be specified
-    genus: "Citrus"  # Mandatory!
-    species: "sinensis" # Mandatory!
-    sex: "male"
-    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)
+    genus: Citrus  # Mandatory!
+    species: sinensis # Mandatory!
+    sex: male
+    strain:
+    common_name:
+    origin:
+    # Useful when there are multiple strains for the same species: set to "yes" to define the strain used as home for JBrowse
+    # main_species: yes
   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!
-    proteins_path: "" # Mandatory!
-    gff_path: "/path/to/repo/examples/src_data/annotation/v1.0/Citrus_sinensis-orange1.1g015632m.g.gff3" # Mandatory!
-    interpro_path: "/path/to/repo/examples/src_data/annotation/v1.0/functional_annotation/Citrus_sinensis-orange1.1g015632m.g.iprscan.xml"
-    orthofinder_path: ""
-    blastp_path: ""
-    blastx_path: "/path/to/repo/examples/src_data/annotation/v1.0/functional_annotation/Blastx_citrus_sinensis-orange1.1g015632m.g.fasta.0_vs_uniprot_sprot.fasta.out"
+    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!
+    proteins_path: # Mandatory!
+    gff_path: /path/to/repo/examples/src_data/annotation/v1.0/Citrus_sinensis-orange1.1g015632m.g.gff3 # Mandatory!
+    interpro_path: /path/to/repo/examples/src_data/annotation/v1.0/functional_annotation/Citrus_sinensis-orange1.1g015632m.g.iprscan.xml
+    orthofinder_path:
+    blastp_path:
+    blastx_path: /path/to/repo/examples/src_data/annotation/v1.0/functional_annotation/Blastx_citrus_sinensis-orange1.1g015632m.g.fasta.0_vs_uniprot_sprot.fasta.out
     # If the user has several datasets of the same 'nature' (gff, genomes, ...) to upload to galaxy, the next scalar is used by the script to differentiate
     # between these different versions and name directories according to it and not overwrite the existing data
     # If left empty, the genome will be considered version "1.0"
-    genome_version: "1.0"
+    genome_version: 1.0
     # Same as genome version, but for the OGS analysis
-    ogs_version: "1.0"
-    performed_by: ""
+    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
-    blast: "False"
-    wiki: "False"
-    apollo: "False"
\ No newline at end of file
+  # List the optional services to be deploy in the stack
+  # By default, only tripal, tripaldb, galaxy, jbrowse and elasticsearch services will be deployed
+    blast: 0
\ No newline at end of file