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Commit b42a7aa8 authored by Loraine Gueguen's avatar Loraine Gueguen
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Update citrus_sinensis.yml

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2 merge requests!9Release 2.0 (merge dev to master),!8Release 2.0
# Input file for the automated creation GGA docker stacks # 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 # 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
- name: citrus_sinensis # Dummy value to designate the species (isn't used by the script) - name: citrus_sinensis
description: description:
# Species description, leave blank if unknown or you don't want it to be used # 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 # These parameters are used to set up the various urls and adresses in different containers
...@@ -13,11 +12,8 @@ ...@@ -13,11 +12,8 @@
strain: "" strain: ""
common_name: "" common_name: ""
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) # Paths to the different datasets to copy and import into the galaxy container (as a shared library)
# Must be absolute paths to the dataset # Must be absolute paths to the dataset
genome_path: "/path/to/repo/examples/src_data/genome/v1.0/Citrus_sinensis-scaffold00001.fasta" # Mandatory! 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! transcripts_path: "/path/to/repo/examples/src_data/annotation/v1.0/Citrus_sinensis-orange1.1g015632m.g.fasta" # Mandatory!
...@@ -35,8 +31,8 @@ ...@@ -35,8 +31,8 @@
ogs_version: "1.0" ogs_version: "1.0"
performed_by: "" performed_by: ""
services: services:
# Describe what optional services to deploy for the stack # List the optional services to be deploy in the stack
# By default, only tripal, tripaldb and galaxy services will be deployed # By default, only tripal, tripaldb, galaxy, jbrowse and elasticsearch services will be deployed
blast: "False" blast: "False"
wiki: "False" wiki: "False"
apollo: "False" apollo: "False"
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