Release 1.0

examples/example.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
+# 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)
+  # 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:
+  # 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"
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