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# Input file for the automated creation GGA docker stacks
# The file consists in a "list" of species for which the script will have to create these stacks/load data into galaxy/run workflows
# This file is internally turned into a list of dictionaries by the scripts
citrus_sinensis: # Dummy value to designate the species (isn't used by the script)
description:
# 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: ""
# the sex and strain, the script will look for files containing the genus, species, sex and strain of the species)
# If no file corresponding to the description is found, this path will be considered empty and the script will
# proceed to the next step (create the directory tree for the GGA docker stack)
data:
# Sequence of paths to the different datasets to copy and import into the galaxy container (as a shared library)
genome_path: "./examples/src_data/genome/v1.0/Citrus_sinensis-scaffold00001.fasta" # Mandatory!
transcripts_path: "./examples/src_data/annotation/v1.0/Citrus_sinensis-orange1.1g015632m.g.fasta" # Mandatory!
proteins_path: "" # Mandatory!
gff_path: "./examples/src_data/annotation/v1.0/Citrus_sinensis-orange1.1g015632m.g.gff3" # Mandatory!
interpro_path: "./examples/src_data/annotation/v1.0/functional_annotation/Citrus_sinensis-orange1.1g015632m.g.iprscan.xml"
orthofinder_path: "/path/to/orthofinder"
blastp_path: "./examples/src_data/annotation/v1.0/functional_annotation/Blastx_citrus_sinensis-orange1.1g015632m.g.fasta.0_vs_uniprot_sprot.fasta.out"
blastx_path: "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"
# Same as genome version, but for the OGS analysis
ogs_version: "1.0"
performed_by: ""
services:
# Describe what optional services to deploy for the stack
# By default, only tripal, tripaldb and galaxy services will be deployed
blast: "False"
wiki: "False"
apollo: "False"