From 74cb81fc00eeed58cbc8b6909e5a7ec875ac84c2 Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Sun, 16 May 2021 14:42:07 +0200
Subject: [PATCH] fix ENABLE_BLAST in gspecies compose. Remove double quotes in
congif input yaml and fix blast value
---
examples/citrus_sinensis.yml | 36 ++++++++++++++++++------------------
gga_init.py | 3 ++-
speciesData.py | 5 +++++
3 files changed, 25 insertions(+), 19 deletions(-)
diff --git a/examples/citrus_sinensis.yml b/examples/citrus_sinensis.yml
index ce35202..0ff6d02 100644
--- a/examples/citrus_sinensis.yml
+++ b/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
diff --git a/gga_init.py b/gga_init.py
index 864b308..879fda8 100755
--- a/gga_init.py
+++ b/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
diff --git a/speciesData.py b/speciesData.py
index 9aff3be..4d4b58a 100755
--- a/speciesData.py
+++ b/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)
--
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