Configuration

The configuration of your DivBrowse instance is managed by a YAML file:

metadata:
  general_description:
  vcf_doi:
  vcf_reference_genome_doi:
  gff3_doi:


datadir: /opt/shape/uwsgi/shape/data/


variants:
  zarr_dir: SNP_matrix_WGS_300_samples.vcf.zarr
  sample_id_mapping_filename:


gff3:
  filename:
  additional_attributes_keys: biotype,gene_id
  feature_type_with_description: gene
  count_exon_variants: true
  key_confidence:
  key_ontology: Ontology_term
  main_feature_types_for_genes_track:
    - gene
    - pseudogene
    - ncRNA_gene
  external_link_ontology_term: https://www.ebi.ac.uk/QuickGO/term/{ID}
  external_links:
    - feature_attribute: ID
      url: https://some.external.resource.org/{FEATURE_ID}
      linktext: Open this gene in an external resource


chromosome_labels:
  1: 1H
  2: 2H
  3: 3H
  4: 4H
  5: 5H
  6: 6H
  7: 7H
  0: Un


gff3_chromosome_labels:
  1: chr1H
  2: chr2H
  3: chr3H
  4: chr4H
  5: chr5H
  6: chr6H
  7: chr7H
  0: chrUn


centromeres_positions:
  1: 205502676
  2: 305853815
  3: 271947776
  4: 282386439
  5: 205989812
  6: 260041240
  7: 328847863
  0: 0


blast:
  active: false
  galaxy_server_url: https://galaxy-web.ipk-gatersleben.de
  galaxy_user:
  galaxy_pass:
  galaxy_tool_id: ncbi_blastn_wrapper_barley
  blast_database: morex_v3
  blast_type: megablast
  blast_result_to_vcf_chromosome_mapping:
    chr1H: 1
    chr2H: 2
    chr3H: 3
    chr4H: 4
    chr5H: 5
    chr6H: 6
    chr7H: 7
    chrUn: 0