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

templates/organisms.yml.j2

-- name: {{ name }}
-  description:
-    genus: {{ genus }}
-    species: {{ species }}
-    sex: {{ sex }}
-    strain: {{ strain }}
-    common_name: {{ common_name }}
-    origin: {{ origin }}
-    {% if main_species is defined and main_species is sameas true %}
-    main_species: yes
+- {{ org_param_name  }}: {{ org_param_name_value }}
+  {{ org_param_desc }}:
+    {{ org_param_desc_genus }}: {{ org_param_desc_genus_value }}
+    {{ org_param_desc_species }}: {{ org_param_desc_species_value }}
+    {{ org_param_desc_sex }}: {{ org_param_desc_sex_value }}
+    {{ org_param_desc_strain }}: {{ org_param_desc_strain_value }}
+    {{ org_param_desc_common_name }}: {{ org_param_desc_common_name_value }}
+    {{ org_param_desc_origin }}: {{ org_param_desc_origin_value }}
+    {% if org_param_desc_main_species_value is defined and org_param_desc_main_species_value is sameas true %}
+    {{ org_param_desc_main_species }}: yes
     {% endif %}
-  data:
-    genome_path: {{ genome_path }}
-    transcripts_path: {{ transcripts_path }}
-    proteins_path: {{ proteins_path }}
-    gff_path: {{ gff_path }}
-    interpro_path: {{ interpro_path }}
-    orthofinder_path: {{ orthofinder_path }}
-    blastp_path: {{ blastp_path }}
-    blastx_path: {{ blastx_path }}
-    genome_version: {{ genome_version }}
-    ogs_version: {{ ogs_version }}
-    performed_by: {{ performed_by }}
-  services:
-    blast: {{ blast }}
\ No newline at end of file
+  {{ org_param_data }}:
+    {{ org_param_data_genome_path }}: {{ org_param_data_genome_path_value }}
+    {{ org_param_data_transcripts_path }}: {{ org_param_data_transcripts_path_value }}
+    {{ org_param_data_proteins_path }}: {{ org_param_data_proteins_path_value }}
+    {{ org_param_data_gff_path }}: {{ org_param_data_gff_path_value }}
+    {{ org_param_data_interpro_path }}: {{ org_param_data_interpro_path_value }}
+    {{ org_param_data_orthofinder_path }}: {{ org_param_data_orthofinder_path_value }}
+    {{ org_param_data_blastp_path }}: {{ org_param_data_blastp_path_value }}
+    {{ org_param_data_blastx_path }}: {{ org_param_data_blastx_path_value }}
+    {{ org_param_data_genome_version }}: {{ org_param_data_genome_version_value }}
+    {{ org_param_data_ogs_version }}: {{ org_param_data_ogs_version_value }}
+    {{ org_param_data_performed_by }}: {{ org_param_data_performed_by_value }}
+  {{ org_param_services }}:
+    {{ org_param_services_blast }}: {{ org_param_services_blast_value }}
\ No newline at end of file