ensembl_rest_testing.conf

#These are settings used to control our test suites. Please do not edit unless you know what you are doing

name = EnsEMBL::REST
default_view = HTML

service_name = Ensembl REST API
service_logo = /static/img/e-ensembl.png
service_parent_url = http://www.ensembl.org
copyright_footer = <a href='http://www.sanger.ac.uk'>WTSI</a> &amp; <a href='http://www.ebi.ac.uk'>EBI</a>

jsonp=1

<Model::Registry>
  skip_initation = 1
  preload = 0
</Model::Registry>

<Model::Documentation>
  paths=[root/documentation]
  
  <replacements>
    gene_stable_id=ENSG00000176515
    gene_stable_id_2=ENSG00000248378
    transcript_stable_id=ENST00000288602
    exon_stable_id=ENSE00001154485
    translation_stable_id=ENSP00000288602
    
    gene_symbol=AL033381.1
    gene_symbol_db=Clone_based_ensembl_gene
    transcript_symbol_db=PDB
    
    prediction_transcript_stable_id=GENSCAN00000000001
    other_features_transcript_stable_id=CCDS5863.1
    
    sequence_region_name=6
    sequence_region=X:1_100_000..1_100_100:1
    sequence_region_negative=X:1_100_000..1_100_100:1
    sequence_region_strandless=X:1_100_000..1_100_100
    contig_sequence_region=AF274858.3.1:1..100
    contig_coord_system=seqlevel
    
    species=homo_sapiens
    species_common=homo_sapiens
    
    taxon=9606
    target_taxon=10090
    target_species=bos_taurus
    
    compara=vertebrates
    compara_method=EPO
    compara_method_type=GenomicAlign
    compara_hom_format=full
    compara_hom_type=all
    compara_aligned=1
    compara_sequence=protein
    compara_cigar_line=1
    compara_species_set_group=mammals
    compara_compact=1
    compara_gene_stable_id=ENSG00000173786

    dbnsfp_readme=https://usf.box.com/s/h9mqovab0on1r3hpopwypcjr9i9mf0s3

    genetree_stable_id=???
    
    from_coord_system=GRCh37
    to_coord_system=GRCh38
    
    cdna_coordinates=100..300
    cds_coordinates=1..1000
    translation_coordinates=100..300
    
    variation_region=9:22125503-22125502:1
    variation_allele=C
    variation_region_two=1:6524705:6524705
    variation_allele_two=T
    
    variation_id=tmp__
    variation_id_two=tmp__

    biotype_group=coding
    biotype_name=protein_coding
    biotype_ot=gene

  </replacements>
</Model::Documentation>

<Controller::Sequence>
  # Set to limit the maximum allowed size of sequence to return from the service. 
  # This will impact on memory footprint so tread carefully
  max_slice_length = 30000
</Controller::Sequence>

<Controller::Overlap>
  # Set to limit the maximum allowed size of feature slices to return from the service. 
  # This will impact on memory footprint so tread carefully
  max_slice_length = 1100000
</Controller::Overlap>

<Controller::VEP>
    fasta = __path_to(t/test-genome-DBs/testdata/vep/7.fa.gz)__
    dir   = __path_to(t/test-genome-DBs/testdata/vep)__
    cache_version     = 86
    cache             = 1
    failed            = 0
    sift              = b
    polyphen          = b
    symbol            = 1
    regulatory        = 1
    biotype           = 1
    check_existing    = 1
    max_post_size     = 10
    warning_file      = STDERR # controls VEP logging, not Catalyst
    plugin_config     = __path_to(t/test-genome-DBs/testdata/vep_plugin_config.txt)__
    dir_plugins       = __path_to(t/test-genome-DBs/testdata/)__
</Controller::VEP>

<View::GFF3>
  default_source=wibble
</View::GFF3>

<Plugin::Cache>
  <backend>
    #Default 
    class = CHI
    driver = Memory
    global = 1
  </backend>
</Plugin::Cache>


<Model::ga4gh::ga4gh_utils>
   ga_config = __path_to(t/test-genome-DBs/testdata/ga_data/ga_vcf_config.json)__ 
   geno_dir  = __path_to(t/test-genome-DBs/testdata/ga_data/)__
   ga_reference_config = __path_to(t/test-genome-DBs/testdata/ga_data/ga_references.json)__ 
</Model::ga4gh::ga4gh_utils>


<Model::Variation>
  use_vcf    = 1
  vcf_config = __path_to(t/test-genome-DBs/testdata/haplotypes_vcf_config.json)__
  dir = __path_to(t/test-genome-DBs/testdata/)__
</Model::Variation>

<Model::Compara>
  species_set_group = mammals
  method            = EPO
  no_branch_lengths = 0
  compact           = 1
  aligned           = 1
  cigar_line        = 1
  format            = full
  sequence          = protein
  type              = all
</Model::Compara>

<Model::LDFeatureContainer>
  use_vcf = 1
  vcf_config = __path_to(t/test-genome-DBs/testdata/ld_vcf_config.json)__
  dir = __path_to(t/test-genome-DBs/testdata/)__
</Model::LDFeatureContainer>