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Commit af80629d authored by Loraine Gueguen's avatar Loraine Gueguen
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2 merge requests!9Release 2.0 (merge dev to master),!6Todo release 1.1
{{ name }}: # Dummy value to designate the species (isn't used by the script) {{ name }}:
description: description:
# Species description, leave blank if unknown or you don't want it to be used genus: {{ genus }} # Mandatory!
# 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: {{ genus }} # Mandatory!
species: {{ species }} # Mandatory! species: {{ species }} # Mandatory!
sex: {{ sex }} sex: {{ sex }}
strain: {{ strain }} strain: {{ strain }}
common_name: {{ common_name }} common_name: {{ common_name }}
origin: {{ origin }} origin: {{ 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: 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: {{ genome_path }} # Mandatory! genome_path: {{ genome_path }} # Mandatory!
transcripts_path: {{ transcripts_path }} # Mandatory! transcripts_path: {{ transcripts_path }} # Mandatory!
proteins_path: {{ proteins_path }} # Mandatory! proteins_path: {{ proteins_path }} # Mandatory!
gff_path: {{ gff_path }} # Mandatory! gff_path: {{ gff_path }} # Mandatory!
interpro_path: {{ interpro_path }} interpro_path: {{ interpro_path }}
orthofinder_path: {{ orthofinder_path }} orthofinder_path: {{ orthofinder_path }}
blastp_path: {{ blastp_path }} blastp_path: {{ blastp_path }}
blastx_path: {{ blastx_path }} blastx_path: {{ blastx_path }}
# 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: {{ genome_version }} genome_version: {{ genome_version }}
# Same as genome version, but for the OGS analysis
ogs_version: {{ ogs_version }} ogs_version: {{ ogs_version }}
performed_by: {{ performed_by }} performed_by: {{ performed_by }}
services: services:
# Describe what optional services to deploy for the stack
# By default, only tripal, tripaldb and galaxy services will be deployed
blast: {{ blast }} blast: {{ blast }}
wiki: {{ wiki }} wiki: {{ wiki }}
apollo: {{ apollo }} apollo: {{ apollo }}
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