/
vectorbase_rest.conf.default
executable file
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/
vectorbase_rest.conf.default
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# This is the default configuration for Ensembl REST applications. Take your own copy
# and make it available to Catalyst via the ENSEMBL_REST_CONFIG or CATALYST_CONFIG ENV vars.
name = EnsEMBL::REST
default_view = HTML
service_name = VectorBase REST API
service_logo = /rest/static/img/vectorbase.png
service_parent_url = http://www.vectorbase.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>
###### Database settings. Use if you want to connect to a single database instance. Common options are given below
host = localhost
port = 3306
user = ensro
version = 93
# verbose = 0
###### Registry file settings
# The file to use as a registry file passed into Bio::EnsEMBL::Registry::load_all()
# file = reg.pm
###### Bio::EnsEMBL::LookUp settings. Used for the bacteira databases provided by Ensembl Genomes
# Load lookup from a local file
# lookup_file = file.json
# Load lookup from a remote URL. Most common option
# lookup_url = http://bacteria.ensembl.org/registry.json
# Store the local loookup cache in a location other than the default (lookup_cache.json)
# lookup_cache_file = lookup_cache.json
# Turn off the local lookup cache storage.
# lookup_no_cache = 1
# Turns on per-process connection sharing; experimental feature but is stable.
# Results in 1 connection per db per process rather than 1 connection per DBAdaptor instance per process
connection_sharing = 1
# Control the reconnection timeout (example is set to 10 mintues in ms). Only works when connection_sharing is on
reconnect_interval = 600000
# Control if we close DB connections down once finished with them. If you are not using the
# connection_sharing it is recommened to turn this on to avoid DOS attacks from your web processes
disconnect_if_idle = 0
# Control if we attempt pings and re-connections before queries. Useful for long running connections
# if you are using connection_sharing
reconnect_when_lost = 1
# Set to control internal Ensembl API caching. Turn this off if your application is persistent (internal
# caches are not shared, will rarely hit and increase your PSGI processes memory footprint)
no_caching = 1
</Model::Registry>
<Model::Lookup>
# Model to use for ID lookups. Currently defaults to the DatabaseIDLookup which can be stable_ids schema
# or a simple DBAdaptor loop lookup
# lookup_model = DatabaseIDLookup
</Model::Lookup>
<Model::Documentation>
#Must be an array reference; if you specify only 1 then surround with [] brackets; if you specify more then remove them
paths=root/documentation
paths=../vectorbase-rest/root/documentation
#How long examples stay in the backend caches before being expired; default is 1hr in seconds.
#Expire depends on the type of CHI cache configured in Plugin::Cache section
# example_expire_time=3600
#Used to control the parameters used in examples. Please edit as you see fit for your infrastructure
<replacements>
genome_name=anopheles_gambiae
gene_stable_id=AGAP004707
gene_stable_id_2=AGAP004727
transcript_stable_id=AGAP004707-RA
transcript_stable_id_2=AGAP004707-RA
exon_stable_id=AGAP004707-RA-E1
translation_stable_id=AGAP004707-PA
vcf=21 26960070 rs116645811 G A . . .
vcf2=21 26965148 rs1135638 G A . . .
gene_symbol=para
gene_symbol2=Gr25
gene_symbol_db=VB_Community_Annotation
transcript_symbol_db=GO
prediction_transcript_stable_id=SNAP_ANOPHELES00000000001
other_features_transcript_stable_id=vb_estt000002
sequence_region_name=2L
sequence_region=2L:2000000-2000100:1
sequence_region_negative=2L:2000000-2000100:-1
sequence_region_strandless=2L:2000000-2000100
contig_sequence_region=AAAB01000001.1
contig_coord_system=scaffold
species=anopheles_gambiae
species_common=Anopheles_gambiae
taxon=7165
taxon_name=Anopheles
taxon_nameish=%25gambiae
target_taxon=7159
target_species=aedes_aegypti
ontology=GO
ontology_term_id=GO:0005248
ontology_term_name=voltage-gated sodium channel activity
compara=vb
compara_method=LASTZ_NET
compara_method_type=GenomicAlign
compara_species_set_1=anopheles_gambiae
compara_species_set_2=anopheles_farauti
genetree_stable_id=VBGT00750000029133
asm_species=anopheles_farauti
asm_sequence_region=KI915068:100000-100100:1
from_coord_system=AfarF2
to_coord_system=AfarF1
cdna_coordinates=100..300
cds_coordinates=1..1000
translation_coordinates=100..300
variation_region=2L:2422152-2423152
variation_allele=A
variation_region_two=2R:56644-57644
variation_allele_two=A
variation_region_three=2L:83084-84084
variation_allele_three=A
# maybe not needed?
variation_id=2L.2422652
variation_id_two=2R.57144
variation_id_three=2L.2402774
variation_id_four=2L.2402774
# replacements for above?
variation_id1=rs180291650
variation_id2=rs180291673
variation_id3=2L.2402774
variation_id4=2L.2402774
vep_hgvs=2L:g.2422652A>T
ld_sequence_region=2L:2269888-2519887
ld_population_name=field isolates, Antula, Guinea-Bissau 1993
d_prime=0.666121
window_size=500
genomic_alignment_species=anopheles_gambiae
genomic_alignment_region=2L:2269888-2519887
genomic_alignment_group=collection-vectorbase
info_division=ensembl
</replacements>
</Model::Documentation>
<Model::Variation>
use_vcf = 1
vcf_config = /vectorbase/ebi/config/charlie/vcf_json/DEFAULTS_vcf.json
</Model::Variation>
<Controller::Compara>
default_compara=vb
</Controller::Compara>
<Controller::Archive>
max_post_size = 1000
</Controller::Archive>
<Controller::Lookup>
max_post_size = 1000
</Controller::Lookup>
<Controller::Taxonomy>
# specify the registry alias for the database containing ncbi_taxa_node tables (normally a compara schema)
taxonomy = vb
</Controller::Taxonomy>
<Controller::Ontology>
# specify the registry alias for the database containing ontology tables (normally called ontology)
ontology = ontology
</Controller::Ontology>
<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 = 1e7
max_post_size = 50
</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 = 5e6
</Controller::Overlap>
<Controller::Homology>
# Sets the default compara to use when finding the best compara fails. Defaults to multi
default_compara=vb
</Controller::Homology>
<!--Controller::Regulatory>
# Sets the default regulation to use when finding the best regulation fails. Defaults to multi
# default_regulation=multi
</Controller::Regulatory-->
<Controller::GenomicAlignment>
# Sets the default compara to use when finding the best compara fails. Defaults to multi
default_compara=vb
</Controller::GenomicAlignment>
<Controller::GeneTree>
# Sets the default compara to use when finding the best compara fails. Defaults to multi
default_compara=vb
</Controller::GeneTree>
<Controller::VEP>
# Supply a fasta path for Human in order to allow VEP to work locally
fasta = Homo_sapiens.GRCh37.75.dna.toplevel.fa # path to Human toplevel fasta file
dir = # path to vep cache directory
# Default parameters for running 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 = 0
biotype = 1
rest = 1
check_existing = 1 # adds some performance penalty, mitigated by tabix-converting the cache (http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#convert)
max_post_size = 1000
</Controller::VEP>
<View::GFF3>
# Set the default source of a GFF3 record
# default_source=.
</View::GFF3>
<Plugin::Cache>
<backend>
#Default
class = CHI
driver = Memory
global = 1
</backend>
</Plugin::Cache>
# add VB static root and give it priority
<Plugin::Static::Simple>
include_path = __path_to(root)__/../../vectorbase-rest/root
include_path = __path_to(root)__
</Plugin::Static::Simple>
# add VB HTML template root and give it priority
<View::HTML>
INCLUDE_PATH = __path_to(root)__/../../vectorbase-rest/root
INCLUDE_PATH = __path_to(root)__
</View::HTML>
# precomputed proteomes controller
<Controller::Proteome>
data_sfx = .json
data_path = /vectorbase/ebi/pep_json
</Controller::Proteome>