fix ENABLE_BLAST in gspecies compose. Remove double quotes in congif input yaml and fix blast value

examples/citrus_sinensis.yml

@@ -6,31 +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"
\ No newline at end of file
+    blast: 0
\ No newline at end of file

gga_init.py

@@ -112,7 +112,8 @@ class DeploySpeciesStack(speciesData.SpeciesData):
         input_vars = {"genus": self.genus_lowercase, "Genus": self.genus_uppercase, "species": self.species,
                       "genus_species": self.genus_species, "genus_species_strain_sex": self.species_folder_name,
                       "genus_species_sex": "{0}_{1}_{2}".format(self.genus_lowercase, self.species.lower(), self.sex),
-                      "strain": self.strain, "sex": self.sex, "Genus_species": self.genus_species[0].upper() + self.genus_species[1:]}
+                      "strain": self.strain, "sex": self.sex, "Genus_species": self.genus_species[0].upper() + self.genus_species[1:],
+                      "blast": self.blast}
         if (len(self.config.keys()) == 0):
             logging.error("Empty config dictionary")
         # Merge the two dicts

speciesData.py

@@ -83,6 +83,11 @@ class SpeciesData:
         self.blastx_path = parameters_dictionary_data[constants.ORG_PARAM_DATA_BLASTX_PATH]
         self.orthofinder_path = parameters_dictionary_data[constants.ORG_PARAM_DATA_ORTHOFINDER_PATH]
 
+        if(constants.ORG_PARAM_SERVICES_BLAST in parameters_dictionary_services.keys()):
+            self.blast = parameters_dictionary_services[constants.ORG_PARAM_SERVICES_BLAST]
+        else:
+            self.blast = "0"
+
         self.genus_lowercase = self.genus[0].lower() + self.genus[1:]
         self.genus_uppercase = self.genus[0].upper() + self.genus[1:]
         self.chado_species_name = "{0} {1}".format(self.species, self.sex)