# 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
ectocarpus_sp2_male:# Dummy value the user gives 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:"ectocarpus"# Mandatory!
species:"sp2"# # 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 galaxy
# Paths must be absolute paths
genome_path:"/path/to/fasta"# Mandatory!
transcripts_path:"/path/to/fasta"# Mandatory!
proteins_path:"/path/to/fasta"# Mandatory!
gff_path:"/path/to/gff"# Mandatory!
interpro_path:"/path/to/interpro"
orthofinder_path:"/path/to/orthofinder"
blastp_path:"/path/to/blastx"
blastx_path:"/path/to/blastp"
# 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:""
performed_by:""
services:
# Describe what optional services to deploy for the stack
# By default, only tripal, tripaldb and galaxy services will be deployed
Arthur Le Bars authored