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abims
e-infra
gga_load_data
Commits
b42a7aa8
Commit
b42a7aa8
authored
3 years ago
by
Loraine Gueguen
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Update citrus_sinensis.yml
parent
524edeff
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2 merge requests
!9
Release 2.0 (merge dev to master)
,
!8
Release 2.0
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examples/citrus_sinensis.yml
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examples/citrus_sinensis.yml
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b42a7aa8
# 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 p
aths to the different datasets to copy and import into the galaxy container (as a shared library)
#
P
aths 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"
\ No newline at end of file
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