From 79c3016c6fab6f17452640bcea5e77d73adbda8b Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Thu, 1 Apr 2021 19:24:23 +0200
Subject: [PATCH] clearer example
---
examples/example.yml | 15 ++++++++-------
1 file changed, 8 insertions(+), 7 deletions(-)
diff --git a/examples/example.yml b/examples/example.yml
index b5f8589..39f05f0 100644
--- a/examples/example.yml
+++ b/examples/example.yml
@@ -18,14 +18,15 @@ citrus_sinensis: # Dummy value to designate the species (isn't used by the scri
# 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)
- genome_path: "./examples/src_data/genome/v1.0/Citrus_sinensis-scaffold00001.fasta" # Mandatory!
- transcripts_path: "./examples/src_data/annotation/v1.0/Citrus_sinensis-orange1.1g015632m.g.fasta" # Mandatory!
+ # Must be absolute paths to the dataset
+ 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!
proteins_path: "" # Mandatory!
- gff_path: "./examples/src_data/annotation/v1.0/Citrus_sinensis-orange1.1g015632m.g.gff3" # Mandatory!
- interpro_path: "./examples/src_data/annotation/v1.0/functional_annotation/Citrus_sinensis-orange1.1g015632m.g.iprscan.xml"
- orthofinder_path: "/path/to/orthofinder"
- blastp_path: "./examples/src_data/annotation/v1.0/functional_annotation/Blastx_citrus_sinensis-orange1.1g015632m.g.fasta.0_vs_uniprot_sprot.fasta.out"
- blastx_path: "Blastx_citrus_sinensis-orange1.1g015632m.g.fasta.0_vs_uniprot_sprot.fasta.out"
+ gff_path: "/path/to/repo/examples/src_data/annotation/v1.0/Citrus_sinensis-orange1.1g015632m.g.gff3" # Mandatory!
+ interpro_path: "/path/to/repo/examples/src_data/annotation/v1.0/functional_annotation/Citrus_sinensis-orange1.1g015632m.g.iprscan.xml"
+ orthofinder_path: ""
+ blastp_path: ""
+ blastx_path: "/path/to/repo/examples/src_data/annotation/v1.0/functional_annotation/Blastx_citrus_sinensis-orange1.1g015632m.g.fasta.0_vs_uniprot_sprot.fasta.out"
# 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"
--
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