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sgn.conf
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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
dbuser web_usr
#dbpass set_this_here
# 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
##### 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
<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
</DatabaseConnection>
### backcompat variables for the various static content types
# relative URL and absolute path for static datasets
static_datasets_url /data
static_datasets_path /data/prod/public
# relative URL and absoluate path for static site content
static_content_url /static_content
static_content_path /data/prod/public/sgn_static_content
homepage_files_dir /data/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>
<View::Email::ErrorEmail>
<default>
content_type text/plain
to sgn-bugs@solgenomics.net
from sgn-bugs@solgenomics.net
charset utf-8
</default>
dump_skip_class Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet DBIx::Class::Row
</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 sgn-feedback@solgenomics.net
feedback_email sgn-feedback@solgenomics.net
bugs_email sgn-bugs@solgenomics.net
email sgn-feedback@solgenomics.net
disable_emails 0
# URL of the cnaonical, 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
# defaults to /tmp/<user>/SGN-site
tempfiles_base
#R qtl tempfiles (must be cluster accessible)
r_qtl_temp_path /data/prod/tmp/r_qtl___USERNAME__
#allow people to log in?
disable_login 0
# where to run cluster jobs
web_cluster_queue
#is this a mirror of SGN, or the real thing?
is_mirror 0
# how to find cosii_files for markerinfo.pl
cosii_files /data/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
# paths to stuff
hmmsearch_location hmmsearch
intron_finder_database /data/prod/public/intron_finder_database
trace_path /data/prod/public/chromatograms
image_dir /images/image_files
image_path /data/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
#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 /data/prod/private/genomes/genefamily/
<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/share/gbrowse/lib/perl5
tmp_dir /var/tmp/gbrowse
cgi_url /gbrowse/bin
static_url /gbrowse/static
run_mode fcgi
cgi_bin /usr/share/gbrowse/cgi-bin
static_dir /usr/share/gbrowse/htdocs
</feature>
# default ITAG config
<feature SGN::Feature::ITAG>
enabled 1
pipeline_base /data/shared/tomato_genome/itagpipeline/itag
</feature>
cview_db_backend cxgn
#how to find blast stuff
blast_path ""
blast_db_path /data/shared/blast/databases/current
#the shared temp directory used by cluster nodes
cluster_shared_tempdir /data/prod/tmp
#how verbose we want the warnings to be in the apache error log
verbose_warnings 1
# Insitu file locations
insitu_fullsize_dir /data/prod/public/images/insitu/processed
insitu_fullsize_url /data/images/insitu/processed
insitu_display_dir /data/prod/public/images/insitu/display
insitu_display_url /data/images/insitu/display
insitu_input_dir /data/prod/public/images/insitu/incoming
#path to our production_ftp site
ftpsite_root /data/prod/public
ftpsite_url ftp://ftp.solgenomics.net
#path to the pucebaboon temperature sensor file:
pucebaboon_file /data/prod/public/digitemp.out