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

gga_get_data.py

@@ -88,18 +88,14 @@ class GetData(speciesData.SpeciesData):
         organism_annotation_dir = os.path.abspath("./src_data/annotation/{0}/OGS{1}".format(self.species_folder_name, self.ogs_version))
         organism_genome_dir = os.path.abspath("./src_data/genome/{0}/v{1}".format(self.species_folder_name, self.genome_version))
 
-        genome_datasets = [constants.ORG_PARAM_DATA_GENOME_PATH]
-        annotation_datasets = [constants.ORG_PARAM_DATA_GFF_PATH,
-                               constants.ORG_PARAM_DATA_TRANSCRIPTS_PATH,
-                               constants.ORG_PARAM_DATA_PROTEINS_PATH,
-                               constants.ORG_PARAM_DATA_INTERPRO_PATH,
-                               constants.ORG_PARAM_DATA_ORTHOFINDER_PATH,
-                               constants.ORG_PARAM_DATA_BLASTP_PATH,
-                               constants.ORG_PARAM_DATA_BLASTX_PATH]
-        # Where to store blast results?
-
-        # search_excluded_datasets = ["interpro_path", "orthofinder_path", "blastp_path", "blastx_path"]  
-        # These datasets will not be searched if missing in the input file
+        genome_datasets = {constants.ORG_PARAM_DATA_GENOME_PATH: self.genome_path}
+        annotation_datasets = {constants.ORG_PARAM_DATA_GFF_PATH: self.gff_path,
+                               constants.ORG_PARAM_DATA_TRANSCRIPTS_PATH: self.transcripts_path,
+                               constants.ORG_PARAM_DATA_PROTEINS_PATH: self.proteins_path,
+                               constants.ORG_PARAM_DATA_INTERPRO_PATH: self.interpro_path,
+                               constants.ORG_PARAM_DATA_ORTHOFINDER_PATH: self.orthofinder_path,
+                               constants.ORG_PARAM_DATA_BLASTP_PATH: self.blastp_path,
+                               constants.ORG_PARAM_DATA_BLASTX_PATH: self.blastx_path}
 
         # Copy datasets in the organism src_data dir tree correct folder
         for k, v in genome_datasets.items():