sgn.conf

#### 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

project_name SGN

# 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>

### Cview configuration parameters
<Controller::Cview>
        cview_default_map_id 9
</Controller::Cview>

### 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>

<Controller::Genomes::Tomato>
   bac_publish_subdir tomato_genome/bacs
</Controller::Genomes::Tomato>

<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  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              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 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            

#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

#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            /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
    releases_base   /data/prod/private/genomes/solanum_lycopersicum/annotation
</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