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wormbase.conf
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######################################################
#
# WormBase Default Configuration
#
# This file contains defaults for the WormBase application.
# It should not be edited. Should you wish to over-ride any
# variables, provide them in a local configuration file
# according to the following rules.
#
# Configuration file precedence (highest to lowest)
#
# 1. Via environment variable provided on the command line
# or in the script/wormbase-init.sh script. For example, the following
# command will load $approot/wormbase_staging.conf with the highest
# precedence.
#
# CATALYST_CONFIG_LOCAL_SUFFIX=staging ./script/wormbase_server.pl -p 8000
#
# 2. Alternatively, provide a local configuration file
# $approot/wormbase_local.conf
#
# 3. This file:
# $approot/wormbase.conf
#
######################################################
######################################################
#
# General
#
######################################################
site_name = WormBase
site_byline = Nematode Information Resource
# Version information
version = 0.02
perl_version = 5.010000
codename = Saag Paneer
# Are we a (development|mirror|local|production) site?
installation_type = production
# For providing Google maps on strain pages
google_api_key = ABQIAAAAX6AZGEUlM28m4mzs0PsGkhRVfLFVmRFz44kSxZwC_XT2TLrxixTVyjZlGBxla25vFXfsh17xrvYj0g
# These all need to be reset and moved outside of version control
facebook_secret_key = a7c919f6d562e140cb6baebe8c7e4a80
facebook_app_id = 145770318837275
twitter_consumer_key = dORNthy42qJmltFfBEplQ
twitter_consumer_secret = ZT89nA5lmc3hGSre14dHSGCcciEPFpOWwCabaM8VUE
# This is the site-wide (dismissable) system message.
# The id is used to make sure a new message won't be hidden
<system_message>
message = "Welcome to WormBase 2 - <a target=\"_blank\" href=\"/tools/support\">need help?</a> <span id=\"fade\">(or visit the <a target=\"_blank\" href=\"http://legacy.wormbase.org\">legacy site</a>)</span>"
id = 2
</system_message>
# 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 = 0
# Are we using a front end proxy in front of our server?
# At WormBase, typically we are (except when running the Catalyst server itself)
using_frontend_proxy = 1
# BASE URL: Not required for default installations
# base = http://www.wormbase.org/
######################################################
#
# 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
######################################################
#
# User Interface
#
######################################################
# Widget timing information.
# Enable display of timing, back end server,
# and cache information. You must also be an
# administrator. Uncommenting disables BOTH
# the collection and display of this information.
timer = 0
########################################################
#
# FILE PATHS
#
########################################################
gbrowse_conf_dir = __path_to(conf)__/gbrowse
tmp_img_base = /tmp
# Where static movies live on the file system TH: no longer in use? 2012.02.06
# static_movie_base = /usr/local/wormbase/website-shared-files/external_datasets
# Where static images (such as the expression renders) live on the file system
# Note: This path served by Static::Simple as specified in Web.pm.
shared_html_base = /usr/local/wormbase/website-shared-files/html
# image_base_classic = /usr/local/wormbase/website-shared-files/html/images-website-classic
########################################################
#
# Cache
#
########################################################
<cache>
enabled 0
default couchdb
<couchdb>
enabled 1
server 127.0.0.1:5984 # defaults
# The production couchdb is located at
# server couchdb.wormbase.org:80 # defaults
# Set this in your wormbase_local.conf if you'd like to use it.
# Note that you MUST specify the port even though it's on 80.
</couchdb>
<memcached>
enabled 0 # not used in code right now
expires 4 weeks
server 206.108.125.168:11211
server 206.108.125.175:11211
server 206.108.125.177:11211
server 206.108.125.178:11211
server 206.108.125.190:11211
</memcached>
<filecache>
enabled 1
root __path_to(root)__/tmp/cache
</filecache>
</cache>
########################################################
#
# EMAILS
#
########################################################
# Issue tracking and reporting
issue_email = help@wormbase.org
# Registering a new account
register_email = oicr@wormbase.org
# For sending emails
no_reply = no-reply@wormbase.org
########################################################
#
# GBrowse
#
########################################################
<WormBase::Web::Controller::GBrowse>
cgi_root_path test
cgi_dir cgi-bin/gb2
# cgi_chain_root /optional/private/path/to/Chained/root
# cgi_file_pattern *
# or regex
cgi_file_pattern /gbrowse/
<CGI>
# username_field username # used for REMOTE_USER env var
pass_env PERL5LIB
pass_env PATH
pass_env /^WORMBASE_/
pass_env GB_HOME
# pass_env GBROWSE_CONF
</CGI>
</WormBase::Web::Controller::GBrowse>
########################################################
#
# API & REST CONFIGURATION
# Should probably be Controller::REST
#
########################################################
<api>
<content_type>
application/json = json
text/xml = xml
text/x-yaml = yml
text/html = html
</content_type>
</api>
########################################################
# Authentication&Authorization: Configuration in Web.pm
########################################################
#<authentication>
# default_realm = members
# <realms>
# <members>
# <credential>
# </credential>
# <store>
# class = DBIx::Class
# user_model = Schema::User
# role_relation = roles
# role_field = role
# #ignore_fields_in_find = remote_name
# #use_userdata_from_session = 1,
# </store>
# </members>
# <openid>
# <credential>
# class = OpenID
# ua_class = LWP::UserAgent
# <extensions>
# http://openid.net/extensions/sreg/1.1
# required = email
# optional = fullname nickname timezone
# </extensions>
# </credential>
# </openid>
# </realms>
#</authentication>
<Model::Schema>
schema_class = WormBase::Schema
<connect_info>
dsn = dbi:mysql:wormbase_user:hostname=localhost
# You can find production here
# dsn = dbi:mysql:wormbase_user:hostname=23.21.171.141
user = wormbase
password =
</connect_info>
</Model::Schema>
password_reset_expires = 86400 # 24 hours
<Model::Mendeley>
<args>
consumer_key = f67b2a45de14e07cc9658f779dd22a5804d32335b
consumer_secret = 1bd1255a50325e72840d33ae8decac11
authorization_url = http://api.mendeley.com/oauth/authorize/
request_token_url = http://api.mendeley.com/oauth/request_token/
access_token_url = http://api.mendeley.com/oauth/access_token/
</args>
</Model::Mendeley>
########################################################
#
# 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
# These are all old precompiled files from CompileGeneResources. None are
# in use any longer
# 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_file_base = ${shared_html_base}
gene_expression_path = /img-static/virtualworm/Gene_Expr_Renders
expression_object_path = /img-static/virtualworm/Expr_Object_Renders
picture = /img-static/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/tmp
#different tools WB provides
<tool>
<blast_blat>
base = /usr/local/wormbase/databases
blast = /blast
blat = /blat
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/blat
#BLAT_CLIENT = /usr/local/wormbase/services/blat/bin/gfClient
</blast_blat>
epic
epcr
gmap
# nearby_genes
nucleotide_aligner
protein_aligner
tree
schema
queries
<ontology_browser>
association_count_file = /usr/local/wormbase/databases/%s/ontology/%s_association.%s.wb
</ontology_browser>
<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 = localhost
user = wormbase
pass =
<data_sources>
clustal = 1
</data_sources>
</mysql>
<gff>
# MySQL configuration
delay = 600
reconnect = 3
# host = localhost mining.wormbase.org
host = localhost
user = wormbase
pass =
<data_sources>
<c_brenneri>
adaptor = dbi::mysqlace
aggregator = wormbase_gene
</c_brenneri>
<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_elegans>
# adaptor = dbi::mysqlace
adaptor = dbi::mysql
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_elegans_pmap>
adaptor = dbi::mysqlace
aggregator = wormbase_gene
</c_elegans_pmap>
<c_elegans_gmap>
adaptor = dbi::mysqlace
aggregator = wormbase_gene
</c_elegans_gmap>
<c_japonica>
adaptor = dbi::mysqlace
aggregator = wormbase_gene
</c_japonica>
<c_remanei>
adaptor = dbi::mysqlace
aggregator = wormbase_gene
</c_remanei>
<p_pacificus>
adaptor = dbi::mysqlace
aggregator = wormbase_gene
</p_pacificus>
</data_sources>
</gff>
</database>
</args>
</Model::WormBaseAPI>
########################################################
#
#
# Plugins
#
#
############################################################
# Error reporting disabled automatically on
# instances with installation_type=development
<stacktrace>
enable 1
</stacktrace>
<Plugin::ErrorCatcher>
enable 1
context 2
</Plugin::ErrorCatcher>
<Plugin::ErrorCatcher::Email>
to oicr@wormbase.org
from todd@wormbase.org
use_tags 1
subject [WB] App error on %h in %F
</Plugin::ErrorCatcher::Email>
# Session database
#<Plugin::Session>
# expires = 3600
# dbi_dbh = Schema
# dbi_table = sessions
# dbi_id_field = session_id
# dbi_data_field = session_data
# dbi_expires_field = expires
#</Plugin::Session>
# Which hash elements of the data structure to return in JSON renders?
<View::JSON>
expose_stash = data
</View::JSON>
########################################################
#
#
# NAVBAR configuration
#
#
############################################################
<nav_bar>
option species
option resources
option tools
</nav_bar>
# Search box dropdown
# A quick list of available searches.
# Remove entries from here to
# prevent them from appearing as an option in the navbar
# global search drop down menu.
# Order is important.
<search_dropdown>
# <option>
# title = Analysis
# id = analysis
# </option>
<option>
title = All
id = all
</option>
<option>
title = Antibody
id = antibody
</option>
<option>
title = Anatomy
id = anatomy_term
</option>
<option>
title = Clone
id = clone
</option>
<option>
title = Expression pattern
id = expr_pattern
</option>
<option>
title = Gene
id = gene
</option>
<option>
title = Gene Class
id = gene_class
</option>
<option>
title = Gene Ontology
id = go_term
</option>
<option>
title = Human Disease
id = disease
</option>
<option>
title = Laboratory
id = laboratory
</option>
<option>
title = Life Stage
id = life_stage
</option>
<option>
title = Phenotype
id = phenotype
</option>
<option>
title = Person
id = person
</option>
<option>
title = Paper
id = paper
</option>
<option>
title = Protein
id = protein
</option>
# <option>
# title = Sequence
# id = sequence
# </option>
<option>
title = Strain
id = strain
</option>
<option>
title = Transgene
id = transgene
</option>
<option>
title = Variation
id = variation
</option>
</search_dropdown>
########################################################
#
#
# Website sections: species, tools, resources, me.
#
# This section configures the available pages, widgets
# and fields for each section of the application.
#
# REMEMBER: If you change the name of anything here,
# you will also need to change the name of the
# corresponding method in the Model class and the name
# of the template
#
############################################################
<sections>
######################################
#
# Species pages.
#
# (Pages available on a per-species
# basis are configured in the
# <species_list> stanza.)
#
######################################
<species>
title = Species
# General structure
# <class_name> -- A symbolic name for the class
# title -- Formal title of the class
# <browse>
# limits =
# limits =
# </browse>
# <search> -- methods to call hen displaying search results
# fields = example
# fields = example2
# </search>
# <widgets>
# <widget1> -- one or more widgets
# name = example -- symbolic name for the widget
# title = My Example -- display name for the widget
# display = [report|index|both] -- where to display the widget (use index for class index, report for summary page)
# tooltip = my tooltip -- brief tooltip, eg: This is a tooltip.
# precache = [0|1] -- boolean whether to precache the page
# fields = examplefield -- one or more fields that correspond to model methods and template name.
# </widget1>
# </widgets>
# <tools> -- list of tools available for this class.
# </tools>
# </class_name>
<anatomy_term>
title = Anatomy term
precache = true
<browse>
limits = Species
limits = Anatomy_term
</browse>
<search>
fields name
fields definition
</search>
<default_widgets>
overview
associations
</default_widgets>
<widgets>
<overview>
name overview
title Overview
tooltip A concise overview of this Anatomy Term
display report
fields name
fields term
fields definition
fields synonyms
fields transgenes
fields expression_patterns
fields gene_ontology
fields anatomy_functions
fields anatomy_function_nots
fields expression_clusters
</overview>
<associations>
name associations
title Associations
tooltip Associations to this Anatomy Term
display report
fields transgenes
fields expression_patterns
fields gene_ontology
fields anatomy_functions
fields anatomy_function_nots
fields expression_clusters
</associations>
<external_links>
name external_links
title External Links
display report
tooltip Links to third party resources.
fields xrefs
</external_links>
<ontology_browser>
name ontology_browser
title Ontology Browser
tooltip Anatomy Term Browser
display report
fields name
</ontology_browser>
</widgets>
<tools>
</tools>
</anatomy_term>
<antibody>
title = Antibody
precache = true
<browse>
limits = Species
limits = Gene_class
</browse>
<search>
fields = name
fields = corresponding_gene
fields = summary
</search>
<default_widgets>
overview
expression
</default_widgets>
<widgets>
<overview>
name overview
title Overview
display report
tooltip A concise overview of the construction and localization of this antibody.
fields name
fields other_names
fields summary
fields corresponding_gene
fields antigen
fields animal
fields clonality
fields laboratory
fields constructed_by
fields remarks
</overview>
<expression>
name expression
title Expression
display report
tooltip Expression patterns generated using the antibody.
fields expression_patterns
</expression>
<references>
name references
title References
display report
tooltip Publications that describe the creation or use of this antibody.
fields references
</references>
</widgets>
<tools>
</tools>
</antibody>
<cds>
title = CDS
precache = true
<browse>
limits = Species
limits = Gene_class
</browse>
<search>
fields = name
fields = taxonomy
fields = description
</search>
<default_widgets>
overview
sequences
</default_widgets>
<widgets>
<overview>
name overview
title Overview
display report
tooltip An overview of the CDS object.
fields name
fields taxonomy
fields description
fields sequence_type
fields identity
fields method
fields remarks
fields corresponding_all
</overview>
<external_links>
name external_links
title External Links
display report
tooltip Links to third party resources.
fields xrefs
</external_links>
<location>
name location
title Location
display report
tooltip The genomic location of the CDS.
fields genomic_position
fields genomic_image
fields tracks
fields genetic_position
</location>
<reagents>
name reagents
title Reagents
display report
tooltip Reagents related to the CDS.
fields microarray_assays
fields orfeome_assays
fields source_clone
fields pcr_products
fields matching_cdnas
</reagents>
<sequences>
name sequences
title Sequences
display report
tooltip Sequences and homologies.
fields print_blast
fields print_sequence
fields print_homologies
fields predicted_exon_structure
fields predicted_units
fields transcripts
</sequences>
</widgets>
<tools>
nucleotide_aligner
</tools>
</cds>
<clone>
title = Clone
precache = true
<browse>
limits = Species
limits = Gene_class
</browse>
<search>
fields = name
fields = type
fields = remarks
</search>
<default_widgets>
overview
location
</default_widgets>
<widgets>
<overview>
name overview
title Overview
display report
tooltip An overview of the clone.
fields name
fields type
fields sequences
fields lengths
fields maps
fields sequence_status
fields canonical_for
fields canonical_parent
fields screened_positive
fields screened_negative
fields gridded_on
fields remarks
fields expression_patterns
fields genomic_positions
</overview>
<external_links>
name external_links
title External Links
display report
tooltip Links to third party resources.
fields xrefs
</external_links>
<location>
name location
title Location
display report
tooltip Genomic location of this clone.
fields genomic_position
fields genomic_image
fields tracks
</location>
<references>
name references
title References
display report
tooltip References that cite this clone.
</references>
</widgets>
<tools>
</tools>
</clone>
<expression_cluster>
title = Expression cluster
precache = true
<browse>
limits = Species
limits = Gene_class
</browse>
<search>
fields = name
fields = algorithm
fields = description
fields = remarks
</search>
<default_widgets>
overview
associations
references
</default_widgets>
<widgets>
<overview>
name overview
title Overview
display report
tooltip A concise overview of the expression cluster.
fields name
fields description
fields remarks
fields algorithm
</overview>
<genes>
name genes
title Genes
display report
tooltip Genes contained in the expression cluster.
fields genes
</genes>
<associations>
name associations
title Associations
display report
tooltip Associated annotations of genes in the expression cluster.
fields anatomy_terms
fields expression_patterns
</associations>
<clustered_data>
name clustered_data
title Clustered data
display report
tooltip Clustered data related to this expression cluster.
fields microarray
fields sage_tags
</clustered_data>
<references>
name references
title References
display report
tooltip References that cite this expression cluster.
</references>
</widgets>
<tools>
</tools>
</expression_cluster>
<expr_pattern>
title = Expression pattern
precache = true
<browse>
limits = Species
limits = Gene_class
</browse>
<search>
fields = name
fields = description
</search>
<advanced_search>
<element>
name = name
type = textbox
</element>
<element>
name = anatomy_term
type = textbox
</element>
<element>
name = life_stage
type = textbox
</element>
</advanced_search>
<default_widgets>
overview
details
references
</default_widgets>
<widgets>
<overview>
name overview
title Overview
display report
tooltip An overview of the expression pattern.
fields name