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ensembl_rest.conf
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ensembl_rest.conf
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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 = 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>
###### Database settings. Use if you want to connect to a single database instance. Common options are given below
# host = useastdb.ensembl.org
# port = 5306
# user = anonymous
#host = ensembldb.ensembl.org
#port = 3337
#user = anonymous
host = SQL_HOST
port = SQL_PORT
user = SQL_USER
# host = ensembl-db
# port = 5306
# user = anonymous
# host = mysql.ebi.ac.uk
# port = 4157
# user = anonymous
version = 84
# 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
# Trigger a preload of the registry the moment the Model::Registry object is contrstructed. Otherwise we
# wait until the 1st request for an adaptor comes in. Use in conjunction with pre-fork PSGI deployments
# to stop registry reload issues
preload = 0
</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]
#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>
gene_stable_id=ENSG00000157764
gene_stable_id_2=ENSG00000248378
transcript_stable_id=ENST00000288602
transcript_stable_id_2=ENST00000513398
exon_stable_id=ENSE00001154485
translation_stable_id=ENSP00000288602
vcf=21 26960070 rs116645811 G A . . .
vcf2=21 26965148 rs1135638 G A . . .
gene_symbol=BRCA2
gene_symbol2=BRAF
gene_symbol_db=HGNC
transcript_symbol_db=PDB
prediction_transcript_stable_id=GENSCAN00000000001
other_features_transcript_stable_id=CCDS5863.1
sequence_region_name=X
sequence_region=X:1000000..1000100:1
sequence_region_negative=X:1000000..1000100:-1
sequence_region_strandless=X:1000000..1000100
contig_sequence_region=ABBA01004489.1:1..100
contig_coord_system=seqlevel
species=homo_sapiens
species_common=human
taxon=9606
taxon_name=Homo sapiens
taxon_nameish=Homo%25
target_taxon=10090
target_ancestral_taxon=9526
target_species=cow
ontology=GO
ontology_term_id=GO:0005667
ontology_term_name=transcription factor complex
compara=multi
compara_method=EPO
compara_method_type=GenomicAlign
genetree_stable_id=ENSGT00390000003602
compara_gene_stable_id=ENSG00000167664
from_coord_system=GRCh37
to_coord_system=GRCh38
cdna_coordinates=100..300
cds_coordinates=1..1000
translation_coordinates=100..300
regulation_id=ENSR00001885035
variation_region=9:22125503-22125502:1
variation_allele=C
variation_region_two=1:6524705:6524705
variation_allele_two=T
variation_region_three=7:100318423-100321323:1
variation_allele_three=DUP
variation_id=rs56116432
variation_id_two=COSM476
variation_id_three=rs1042779
ld_population_name=1000GENOMES:phase_3:KHV
r2=0.85
d_prime=1.0
vep_hgvs=AGT:c.803T>C
vep_hgvs_two=9:g.22125504A>C
vep_hgvs_three=ENST00000003084:c.1431_1433delTTC
genomic_alignment_species=taeniopygia_guttata
genomic_alignment_region=2:106040000-106040050:1
genomic_alignment_group=sauropsids
info_division=ensembl
</replacements>
</Model::Documentation>
<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 = plants
</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=multi
</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=multi
</Controller::GenomicAlignment>
<Controller::Variaton>
max_post_size = 1000
</Controller::Variaton>
<Controller::VEP>
# Supply a fasta path for Human in order to allow VEP to work locally
fasta = /opt/.vep/Homo_sapiens.GRCh37.dna.primary_assembly.fa # path to Human toplevel fasta file (bgzipped)
dir = /opt/.vep/homo_sapiens/84_GRCh37 # 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 = 1
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)
fork = 4
max_post_size = 1000
warning_file = STDERR # controls VEP logging, not Catalyst
plugin_config = # path to plugin config
dir_plugins = # path to VEP_plugins checkout
</Controller::VEP>
<View::GFF3>
# Set the default source of a GFF3 record
# default_source=.
</View::GFF3>
<View::HTML>
# To configure any templates to your own needs provide new includes
# here and replace the template toolkit file. Pay attention to order
# (1st defined is 1st consulted)
# INCLUDE_PATH __path_to(alternative/root)__
INCLUDE_PATH __path_to(root)__
</View::HTML>
<Plugin::Cache>
<backend>
#Default
class = CHI
driver = Memory
global = 1
# Memcache
# driver = Memcached
# namespace = endpoint_examples
# servers = [127.0.0.1:11211]
# debug = 0
# <l1_cache>
# driver = Memory
# global = 1
# max_size = 126976
# </l1_cache>
</backend>
</Plugin::Cache>
<Model::ga4gh::callSet>
ga_config = __path_to(ga_vcf_config.json)__
</Model::ga4gh::callSet>
<Model::ga4gh::variants>
ga_config = __path_to(ga_vcf_config.json)__
</Model::ga4gh::variants>
<Model::ga4gh::variantSet>
ga_config = __path_to(ga_vcf_config.json)__
</Model::ga4gh::variantSet>
<Model::Variation>
use_vcf = 1
vcf_config = __path_to(vcf_config.json)__
</Model::Variation>
<Model::LDFeatureContainer>
use_vcf = 1
vcf_config = __path_to(vcf_config.json)__
</Model::LDFeatureContainer>