From af80629da24f023dc7a428ec777c423d0f033282 Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Mon, 3 May 2021 23:24:21 +0200
Subject: [PATCH] remove comments
---
templates/organisms.yml.j2 | 20 +++-----------------
1 file changed, 3 insertions(+), 17 deletions(-)
diff --git a/templates/organisms.yml.j2 b/templates/organisms.yml.j2
index 98ce0e4..e564629 100644
--- a/templates/organisms.yml.j2
+++ b/templates/organisms.yml.j2
@@ -1,38 +1,24 @@
-{{ name }}: # Dummy value to designate the species (isn't used by the script)
+{{ name }}:
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: {{ genus }} # Mandatory!
+ genus: {{ genus }} # Mandatory!
species: {{ species }} # Mandatory!
sex: {{ sex }}
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:
- # 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!
- transcripts_path: {{ transcripts_path }} # Mandatory!
+ transcripts_path: {{ transcripts_path }} # Mandatory!
proteins_path: {{ proteins_path }} # Mandatory!
gff_path: {{ gff_path }} # Mandatory!
interpro_path: {{ interpro_path }}
orthofinder_path: {{ orthofinder_path }}
blastp_path: {{ blastp_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 }}
- # Same as genome version, but for the OGS analysis
ogs_version: {{ ogs_version }}
performed_by: {{ performed_by }}
services:
- # Describe what optional services to deploy for the stack
- # By default, only tripal, tripaldb and galaxy services will be deployed
blast: {{ blast }}
wiki: {{ wiki }}
apollo: {{ apollo }}
--
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