Release 1.0

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"