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wormbase_local.conf.template
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############################################################
#
# WormBase Local Configuration
#
# This file contains site-specific configuration.
# Values set here will over-ride the defaults.
#
############################################################
######################################################
#
# WormBase Production Configuration
#
# Settings in this file over-ride the default
# wormbase.conf settings when the app is launched
# by starman-production.sh.
#
# See wormbase.conf for a description of directives.
#
######################################################
# What type of installation
installation_type = development
# Google Maps API
google_api_key = ABQIAAAAX6AZGEUlM28m4mzs0PsGkhRVfLFVmRFz44kSxZwC_XT2TLrxixTVyjZlGBxla25vFXfsh17xrvYj0g
# SSL
enable_ssl = 1
# REQUIRED FOR PRODUCTION: Base URL
#base = http://www.wormbase.org/
######################################################
#
# Debugging
#
######################################################
debug = 0
fatal_non_compliance = 0
timer = 0
<stacktrace>
enable 1
</stacktrace>
<Plugin::ErrorCatcher>
enable 1
</Plugin::ErrorCatcher>
<Plugin::ErrorCatcher::Email>
to you@yourdomain.com
from you@yourdomain.com
use_tags 1
# subject Error Report from: %h; %F, line %l
</Plugin::ErrorCatcher::Email>
########################################################
#
# EMAILS
#
########################################################
# Issue tracking and reporting
issue_email = you@youremail.org
# Registering a new account
register_email = you@youremail.org
########################################################
#
# Cache
#
########################################################
# cache_content: Should this webapp try to cache content?
# Uncomment to turn off caching
cache_content = false
# Cache root (pregenerated HTML)
cache_root = /usr/local/wormbase/databases/%s/cache
# By default, we cache to couchdb on localhost
# Production and staging override to cache to web6
# Master Couch
# host = 127.0.0.1
<Model::CouchDB>
host = 206.108.125.165
port = 5984
</Model::CouchDB>
########################################################
#
# Database Locations and Authorization
#
# By default, we use remote data sources for
# convenience but expect this to be overriden
# by the wormbase_local.conf.
#
########################################################
# 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>
<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/shared/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 mining.wormbase.org
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 = 206.108.125.165
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>