diff --git a/examples/input_example.yml b/examples/input_example.yml deleted file mode 100644 index e718673e9de3e25f2412ed777d309121013b0bdd..0000000000000000000000000000000000000000 --- a/examples/input_example.yml +++ /dev/null @@ -1,68 +0,0 @@ -# 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 - blast: "False" - wiki: "False" - apollo: "False" - -# Second example without the explanation -ectocarpus_sp2_female: - description: - genus: "ectocarpus" - species: "sp2" - sex: "female" - strain: "" - common_name: "" - origin: "" - data: - genome_path: "/path/to/fasta" - transcripts_path: "/path/to/fasta" - proteins_path: "/path/to/fasta" - gff_path: "/path/to/gff" - interpro_path: "/path/to/interpro" - orthofinder_path: "/path/to/orthofinder" - blastp_path: "/path/to/blastx" - blastx_path: "/path/to/blastp" - genome_version: "1.0" - ogs_version: "1.0" - performed_by: "" - services: - blast: "False" - wiki: "False" - apollo: "False" \ No newline at end of file