Release_2.0 next

General

• Move constants to file constants.py
• Set default config file in scripts.
• Update description of scripts in main.
• Update README.md

Input config file

• Change config root to dict and update parse_config().
• Change some config parameters name (galaxy_persist_data, tripal_banner_path, jbrowse_menu_url), update example config file and compose templates.
• Remove apollo config variables (webapollo_user, webapollo_password) in config file and in gspecies compose template, because apollo service not deployed here.

Utilities.py

• Factorize parse_input() et parse_config().
• Get input yml keys from constants (update organisms.yml.j2 and add create_org_param_dict_from_constants())

gspecies_compose.yml

• set ENABLE_WIKI and ENABLE_APOLLO to 0 in gspecies compose template
• fix ENABLE_BLAST value in gspecies compose template

gga_get_data.py

• Remove useless variable datasets_to_get

gga_init.py

• replace subprocess.call() with subprocess.run(). Factorize run_command() and run_docker_stack_deploy()
• fix banner copy

examples/citrus_sinensis.yml

@@ -6,33 +6,31 @@
   # 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: ""
+    genus: Citrus  # Mandatory!
+    species: sinensis # Mandatory!
+    sex: male
+    strain:
+    common_name:
+    origin:
   data:
   # 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:
   # 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
+    blast: 0
\ No newline at end of file