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sgn.conf
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#### most commonly altered config variables ####
#is this a production server?
production_server 0
#default database connection info
dbhost db.sgn.cornell.edu
dbname cxgn-test
dbuser web_usr
#dbpass set_this_here
vigs_tool_blast_datasets 148 149 196 69
project_name SGN
disable_login 0
# who is the web server user for chowning and emailing. need to set
# these manually under Apache mod_perl for example, because the server
# runs under a different user than when it starts.
www_user __USERNAME__
www_group __GROUPNAME__
# when true, server removes its tempfiles when the app is started
clear_tempfiles_on_restart 1
r_qtl_temp_path /static/documents/tempfiles/solqtl/__USERNAME__
##### other config variables #####
dbsearchpath sgn
dbsearchpath public
dbsearchpath annotation
dbsearchpath genomic
dbsearchpath insitu
dbsearchpath metadata
dbsearchpath pheno_population
dbsearchpath phenome
dbsearchpath physical
dbsearchpath tomato_gff
dbsearchpath biosource
dbsearchpath gem
dbsearchpath sgn_people
<DatabaseConnection sgn_test>
#password set_this_please
dsn dbi:Pg:host=localhost;dbname=cxgn
user postgres
search_path public
search_path sgn
search_path annotation
search_path genomic
search_path insitu
search_path metadata
search_path pheno_population
search_path phenome
search_path physical
search_path tomato_gff
search_path biosource
search_path gem
search_path sgn_people
</DatabaseConnection>
### Cview configuration parameters
<Controller::Cview>
cview_default_map_id 9
</Controller::Cview>
## captcha keys for the production site
captcha_private_key 6Lc__9YSAAAAANcTczARhRnZRkKmzWjnhipyqI6f
captcha_public_key 6Lc__9YSAAAAAH2ODL2FlR8jKa2Ms9i9d_0ziBWr
contact_form_human_question 2+3
contact_form_human_answer 5
### backcompat variables for the various static content types
# relative URL and absolute path for static datasets
static_datasets_url /data
static_datasets_path /export/prod/public
# relative URL and absoluate path for static site content
static_content_url /static_content
static_content_path /export/prod/public/sgn_static_content
homepage_files_dir /export/prod/public/sgn_static_content/homepage
# this needs to be here rather than in the CGI controller itself to
# work around a bug in all but the most recent
# Catalyst::Controller::CGIBin
<Controller::CGI>
cgi_dir __path_to(cgi-bin)__
</Controller::CGI>
<Controller::Genomes::Tomato>
bac_publish_subdir tomato_genome/bacs
</Controller::Genomes::Tomato>
<Plugin::SmartURI>
disposition host-header # application-wide
uri_class URI::SmartURI # by default
</Plugin::SmartURI>
<View::Email::ErrorEmail>
<default>
content_type text/plain
from [email protected]
charset utf-8
</default>
dump_skip_class Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet DBIx::Class::Row HTML::Mason::Interp
</View::Email::ErrorEmail>
# should we send emails, if we are a production server? this can be
# used to turn off emails if we are being bombarded.
admin_email [email protected]
feedback_email [email protected]
bugs_email [email protected]
email [email protected]
contact_form_email [email protected]
tokn_email [email protected]
disable_emails 0
# URL of the canonical, main production site
main_production_site_url http://solgenomics.net
#is there a system message text file somewhere we should be displaying?
system_message_file __HOME__/system_message.txt
# defaults to /tmp/<user>/SGN-site
#tempfiles_base
tempfiles_base ""
#
# where to run cluster jobs - nothing means "batch" queue
#web_cluster_queue
# where to run cluster jobs
web_cluster_queue batch
#is this a mirror of SGN, or the real thing?
is_mirror 0
#
# how to find cosii_files for markerinfo.pl
cosii_files /export/cosii2
#
# log files, ABSOLUTE PATHS
error_log /var/log/sgn-site/error.log
access_log /var/log/sgn-site/access.log
rewrite_log /var/log/sgn-site/rewrite.log
blast_log /export/prod/tmp/blast/blast.log
#
# paths to stuff
hmmsearch_location hmmsearch
intron_finder_database /export/prod/public/intron_finder_database
#
trace_path /export/prod/public/chromatograms
image_dir /images/image_files
image_path /export/prod/public/images
tempfiles_subdir /static/documents/tempfiles
submit_dir /data/shared/submit-uploads
programs_subdir /programs
documents_subdir /documents
conf_subdir /conf
support_data_subdir /support_data
#
#stock tempfiles (for downloading phenotype and genotype raw data)
stock_tempfiles /static/documents/tempfiles/stock
#
#currently our cookies encrypt stuff, so this is just a random string to use to do that
cookie_encryption_key bo9yie2JeeVee6ouAhch9aomeesieJ3iShae8aa8
#
# where the genefamily info is stored
genefamily_dir /export/prod/private/genomes/genefamily/
#
# the right ontology db name for the trait search
trait_ontology_db_name SP
onto_root_namespaces GO (Gene Ontology), PO (Plant Ontology), SO (Sequence Ontology), PATO (Phenotype and Trait Ontology), SP (Solanaceae Ontology)
##
<feature SGN::Feature::FeaturePages>
enabled 1
</feature>
<feature SGN::Feature::LocusPages>
enabled 1
</feature>
#
# default GBrowse2 configuration, for a Debian gbrowse2 installation
<feature SGN::Feature::GBrowse2>
enabled 1
perl_inc /usr/local/share/website/gbrowse/lib/perl5
tmp_dir /usr/local/share/website/tmp/gbrowse
cgi_url /gbrowse/bin
static_url /gbrowse/static
run_mode fastcgi
cgi_bin /usr/lib/cgi-bin/gbrowse
static_dir /usr/local/share/website/gbrowse/htdocs
</feature>
#
# default ITAG config
<feature SGN::Feature::ITAG>
enabled 1
pipeline_base /export/shared/tomato_genome/itagpipeline/itag
releases_base /export/prod/private/genomes/solanum_lycopersicum/annotation
</feature>
#
cview_db_backend cxgn
#
#how to find blast stuff
blast_path ""
blast_db_path /export/prod/blast/databases/current
vigs_tool_blast_datasets 148 149 196 69
#
#bin directory used by cluster nodes
cluster_shared_bindir /export/prod/bin
#
#the shared temp directory used by cluster nodes
cluster_shared_tempdir /export/prod/tmp
gbs_temp_data /export/prod/public
#
#how verbose we want the warnings to be in the apache error log
verbose_warnings 1
#
# Insitu file locations
insitu_fullsize_dir /export/prod/public/images/insitu/processed
insitu_fullsize_url /export/images/insitu/processed
insitu_display_dir /export/prod/public/images/insitu/display
insitu_display_url /export/images/insitu/display
insitu_input_dir /export/prod/public/images/insitu/incoming
#
#path to our production_ftp site
ftpsite_root /export/prod/public
ftpsite_url ftp://ftp.solgenomics.net
#path to the pucebaboon temperature sensor file:
pucebaboon_file /export/prod/public/digitemp.out
#
#path for archving uploaded files
archive_path /export/prod/sgn_archive
#site overall identifier prefix used for site specific data
#such as stocks, unignes (yet to be implemented) and other datatypes
#for example, uploading barcode phenotyping data will not work without this key (see L<CXGN::Stock::StockBarcode> )
identifier_prefix SGN