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ensembl_rest_testing.conf
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ensembl_rest_testing.conf
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#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> & <a href='http://www.ebi.ac.uk'>EBI</a>
jsonp=1
<Model::Registry>
skip_initation = 1
</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=multi
compara_method=EPO
compara_method_type=GenomicAlign
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__
</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/human_vep/7.fa)__
dir = __path_to(t/test-genome-DBs/testdata/human_vep)__
cache_region_size = 1000000
chunk_size = 50000
whole_genome = 1
compress = gzip -dc
terms = SO
cache = 1
failed = 0
core_type = core
quiet = 1
sift = b
polyphen = b
symbol = 1
regulatory = 1
check_existing = 1
rest = 1
biotype = 1
max_post_size = 10
warning_file = STDERR # controls VEP logging, not Catalyst
</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>