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wormbase_cloud.conf
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######################################################
#
# WormBase Default Configuration
#
# This file contains defaults for the WormBase
# application. This file should not be edited.
#
# Configuration file precedence (lowest to highest)
#
# $approot/wormbase.conf // this file
#
# You can over-ride the default settings in this file in:
# $approot/wormbase_local.conf // local defaults
#
# Finally, you can provide your own local config file at
# $approot/wormbase_[whatever].conf
# shell> export WormBase_LOCAL_CONFIG_SUFFIX=[whatever]
#
# For production servers, we dynamically select a configuration file
# using this trick.
# $approot/wormbase_[hostname].conf // local defaults (for deployment)
# $approot/wormbase_[developer].conf // developer defaults
#
######################################################
# Are we a (development|mirror|local|production) site?
installation_type = production
# For providing Google maps on strain pages
google_api_key = ABQIAAAAX6AZGEUlM28m4mzs0PsGkhRVfLFVmRFz44kSxZwC_XT2TLrxixTVyjZlGBxla25vFXfsh17xrvYj0g
# enable_ssl = 1;
# secure_uri_for will return the uri with the scheme https
# enable_ssl = 0;
# secure_uri_for will return the results of uri_for
enable_ssl = 1
######################################################
#
# Debugging
#
######################################################
# debug: enable system-wide debugging; expects boolean
debug = 0
# debug_view: style of the view debugging. Off by default
# unless "debug" is set above and debug_view set to
# one of
# comment - send debugging statements as HTML comments
# browser - send debugging statements in formatted divs
# log - send to the error log file
debug_view =
# Enable fatal data stucture compliance. Rendering of
# widgets will fail if the installation_type is 'development'
# and if this is set to a true value.
fatal_non_compliance = 0
timer = 0
########################################################
#
# EMAILS
#
########################################################
# Issue tracking and reporting
issue_email = help@wormbase.org
# Registering a new account
register_email = staff@wormbase.org
# wormbase_user exists only on wb-web6 (206.108.125.165)
<Model::Schema>
schema_class = WormBase::Schema
<connect_info>
dsn = dbi:mysql:wormbase_user:hostname=localhost
user = wormbase
password =
</connect_info>
</Model::Schema>
########################################################
#
# Database Locations and Authorization
#
# By default, we use remote data sources for
# convenience but expect this to be overriden
# by the wormbase_local.conf.
#
########################################################
<Model::WormBaseAPI>
class = WormBase::API
<args>
<pre_compile>
base = /usr/local/wormbase/databases/
gene = /gene/
position_matrix = /position_matrix/
rnai_details_file = rnai_data.txt
gene_rnai_phene_file = gene_rnai_pheno.txt
gene_variation_phene_file = variation_data.txt
phenotype_name_file = phenotype_id2name.txt
gene_xgene_phene_file = gene_xgene_pheno.txt
pm_id2consensus_seq_file = pm_id2consensus_seq.txt
pm_id2source_pm_file = pm_id2source_pm.txt
image_base = /usr/local/wormbase/website-shared-files/html/img
# image_base_classic = /usr/local/wormbase/website-shared-files/html/images-website-classic
gene_expr = $image_base/virtualworm/Gene_Expr_Renders
expr_object = $image_base/virtualworm/Expr_Object_Renders
picture = $image_base/picture_object
</pre_compile>
conf_dir = __path_to(conf)__/
# Temporary directory in filesystem space
# tmp_base = __path_to(root)__/tmp/
# tmp_base = /tmp/wormbase/
# In production, this is an nfs mount
tmp_base = /usr/local/wormbase/shared/tmp/
#different tools WB provides
<tool>
<blast_blat>
base = /usr/local/wormbase/databases/
blast = /blast/
SCORE_KEY_IMAGE = score_key.png
HSP_GENOME_LINK_PART_LIMIT = 10
HSP_ALIGNMENT_IMAGE_LIMIT = 10
BLAST_EXEC_DIR = /usr/local/wormbase/services/blast
BLAT_CLIENT = /usr/local/wormbase/services/blat/bin/gfClient
b_genome = c_elegans c_briggsae c_brenneri c_japonica c_remanei b_malayi m_hapla m_incognita p_pacificus h_contortus
b_protein = c_elegans c_briggsae c_brenneri c_japonica c_remanei b_malayi p_pacificus
b_gene = c_elegans c_briggsae
b_est = c_elegans
ARCHIVES = WS100 WS110 WS120 WS130 WS140 WS150 WS160 WS170 WS180 WS190
</blast_blat>
protein_aligner
nucleotide_aligner
tree
<print>
PRO_EXEC = ./CutyCapt
</print>
</tool>
<database>
# tmp directory for sockets and lock files.
# This *must* be distinct from above since
# to prevent collisions of lock files in production.
tmp = /tmp/wormbase/
<acedb>
# Acedb configuration
delay = 600
reconnect = 5
host = localhost
port = 2005
user =
pass =
cache_root = __path_to(root)__/cache/
cache_expires = 3 weeks
cache_size = 100000000
cache_auto_purge_interval =
</acedb>
<mysql>
delay = 600
reconnect = 3
host = localhost
user = wormbase
pass =
<data_sources>
clustal = 1
</data_sources>
</mysql>
<gff>
# MySQL configuration
delay = 600
reconnect = 3
# host = 206.108.125.165
host = localhost
user = wormbase
pass =
<data_sources>
<c_elegans>
adaptor = dbi::mysqlace
aggregator = processed_transcript{coding_exon,5_UTR,3_UTR/CDS}
aggregator = full_transcript{coding_exon,five_prime_UTR,three_prime_UTR/Transcript}
aggregator = transposon{coding_exon,five_prime_UTR,three_prime_UTR}
aggregator = clone
aggregator = alignment
aggregator = waba_alignment
aggregator = coding{coding_exon}
aggregator = pseudo{exon:Pseudogene/Pseudogene}
aggregator = rna{exon/Transcript}
aggregator = wormbase_cds{coding_exon,three_prime_UTR,five_prime_UTR}
aggregator = motif_span{motif_segment/Motif}
</c_elegans>
<c_briggsae>
adaptor = dbi::mysqlace
aggregator = wormbase_cds{coding_exon,three_prime_UTR,five_primer_UTR/CDS}
aggregator = clone
aggregator = alignment
aggregator = waba_alignment
</c_briggsae>
<c_brenneri>
adaptor = dbi::mysqlace
aggregator = wormbase_gene
</c_brenneri>
<c_remanei>
adaptor = dbi::mysqlace
aggregator = wormbase_gene
</c_remanei>
<p_pacificus>
</p_pacificus>
<c_elegans_pmap>
adaptor = dbi::mysqlace
aggregator = wormbase_gene
</c_elegans_pmap>
<c_elegans_gmap>
adaptor = dbi::mysqlace
aggregator = wormbase_gene
</c_elegans_gmap>
</data_sources>
</gff>
</database>
</args>
</Model::WormBaseAPI>
<stacktrace>
enable 1
</stacktrace>
<Plugin::ErrorCatcher>
enable 1
</Plugin::ErrorCatcher>
<Plugin::ErrorCatcher::Email>
to oicr@wormbase.org
from oicr@wormbase.org
use_tags 1
# subject Error Report from: %h; %F, line %l
</Plugin::ErrorCatcher::Email>