citrus_sinensis.yml

# 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

- name: citrus_sinensis
  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: ""
  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"
    # 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:
  # 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"
    wiki: "False"
    apollo: "False"