sgn.conf

   1
   2 #### most commonly altered config variables ####
   3
   4 #is this a production server?
   5 production_server         0
   6
   7 #default database connection info
   8 dbhost   db.sgn.cornell.edu
   9 dbname   cxgn
  10 dbuser   web_usr
  11 #dbpass   set_this_here
  12
  13 # who is the web server user for chowning and emailing.  need to set
  14 # these manually under Apache mod_perl for example, because the server
  15 # runs under a different user than when it starts.
  16 www_user                 __USERNAME__
  17 www_group                __GROUPNAME__
  18
  19 # when true, server removes its tempfiles when the app is started
  20 clear_tempfiles_on_restart  1
  21
  22 ##### other config variables #####
  23
  24 dbsearchpath   sgn
  25 dbsearchpath   public
  26 dbsearchpath   annotation
  27 dbsearchpath   genomic
  28 dbsearchpath   insitu
  29 dbsearchpath   metadata
  30 dbsearchpath   pheno_population
  31 dbsearchpath   phenome
  32 dbsearchpath   physical
  33 dbsearchpath   tomato_gff
  34 dbsearchpath   biosource
  35 dbsearchpath   gem
  36
  37 <DatabaseConnection sgn_test>
  38         #password   set_this_please
  39         dsn   dbi:Pg:host=localhost;dbname=cxgn
  40         user   postgres
  41         search_path   public
  42         search_path   sgn
  43         search_path   annotation
  44         search_path   genomic
  45         search_path   insitu
  46         search_path   metadata
  47         search_path   pheno_population
  48         search_path   phenome
  49         search_path   physical
  50         search_path   tomato_gff
  51         search_path   biosource
  52         search_path   gem
  53 </DatabaseConnection>
  54
  55 ### backcompat variables for the various static content types
  56 # relative URL and absolute path for static datasets
  57 static_datasets_url       /data
  58 static_datasets_path      /data/prod/public
  59
  60 # relative URL and absoluate path for static site content
  61 static_content_url        /static_content
  62 static_content_path       /data/prod/public/sgn_static_content
  63 homepage_files_dir        /data/prod/public/sgn_static_content/homepage
  64
  65 # this needs to be here rather than in the CGI controller itself to
  66 # work around a bug in all but the most recent
  67 # Catalyst::Controller::CGIBin
  68 <Controller::CGI>
  69     cgi_dir   __path_to(cgi-bin)__
  70 </Controller::CGI>
  71
  72 <View::Email::ErrorEmail>
  73     <default>
  74         content_type  text/plain
  75         to            sgn-bugs@solgenomics.net
  76         from          sgn-bugs@solgenomics.net
  77         charset       utf-8
  78     </default>
  79     dump_skip_class   Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet  DBIx::Class::Row
  80 </View::Email::ErrorEmail>
  81
  82 # should we send emails, if we are a production server? this can be
  83 # used to turn off emails if we are being bombarded.
  84 admin_email              sgn-feedback@solgenomics.net
  85 feedback_email           sgn-feedback@solgenomics.net
  86 bugs_email               sgn-bugs@solgenomics.net
  87 email                    sgn-feedback@solgenomics.net
  88 disable_emails           0
  89
  90 # URL of the cnaonical, main production site
  91 main_production_site_url  http://solgenomics.net
  92
  93 #is there a system message text file somewhere we should be displaying?
  94 system_message_file
  95 # defaults to /tmp/<user>/SGN-site
  96 tempfiles_base
  97
  98 #R qtl tempfiles (must be cluster accessible)
  99 r_qtl_temp_path           /data/prod/tmp/r_qtl___USERNAME__
 100
 101 #allow people to log in?
 102 disable_login             0
 103
 104 # where to run cluster jobs
 105 web_cluster_queue
 106
 107 #is this a mirror of SGN, or the real thing?
 108 is_mirror                 0
 109
 110 # how to find cosii_files for markerinfo.pl
 111 cosii_files               /data/cosii2
 112
 113 # log files, ABSOLUTE PATHS
 114 error_log                 /var/log/sgn-site/error.log
 115 access_log                /var/log/sgn-site/access.log
 116 rewrite_log               /var/log/sgn-site/rewrite.log
 117
 118 # paths to stuff
 119 hmmsearch_location        hmmsearch
 120 intron_finder_database    /data/prod/public/intron_finder_database
 121
 122 trace_path                /data/prod/public/chromatograms
 123 image_dir                 /images/image_files
 124 image_path                /data/prod/public/images
 125 tempfiles_subdir          /static/documents/tempfiles
 126 submit_dir                /data/shared/submit-uploads
 127 programs_subdir           /programs
 128 documents_subdir          /documents
 129 conf_subdir               /conf
 130 support_data_subdir       /support_data
 131
 132 #currently our cookies encrypt stuff, so this is just a random string to use to do that
 133 cookie_encryption_key     bo9yie2JeeVee6ouAhch9aomeesieJ3iShae8aa8
 134
 135 # where the genefamily info is stored
 136 genefamily_dir            /data/prod/private/genomes/genefamily/
 137
 138 <feature SGN::Feature::FeaturePages>
 139     enabled      1
 140 </feature>
 141 <feature SGN::Feature::LocusPages>
 142     enabled      1
 143 </feature>
 144
 145 # default GBrowse2 configuration, for a Debian gbrowse2 installation
 146 <feature SGN::Feature::GBrowse2>
 147     enabled      1
 148     perl_inc     /usr/share/gbrowse/lib/perl5
 149     tmp_dir      /var/tmp/gbrowse
 150     cgi_url      /gbrowse/bin
 151     static_url   /gbrowse/static
 152     run_mode     fcgi
 153     cgi_bin      /usr/share/gbrowse/cgi-bin
 154     static_dir   /usr/share/gbrowse/htdocs
 155 </feature>
 156
 157 # default ITAG config
 158 <feature SGN::Feature::ITAG>
 159     enabled         1
 160     pipeline_base   /data/shared/tomato_genome/itagpipeline/itag
 161     releases_base   /data/prod/private/genomes/solanum_lycopersicum/annotation
 162 </feature>
 163
 164 cview_db_backend    cxgn
 165
 166 #how to find blast stuff
 167 blast_path                ""
 168 blast_db_path             /data/shared/blast/databases/current
 169
 170 #the shared temp directory used by cluster nodes
 171 cluster_shared_tempdir    /data/prod/tmp
 172
 173 #how verbose we want the warnings to be in the apache error log
 174 verbose_warnings          1
 175
 176 # Insitu file locations
 177 insitu_fullsize_dir       /data/prod/public/images/insitu/processed
 178 insitu_fullsize_url       /data/images/insitu/processed
 179 insitu_display_dir        /data/prod/public/images/insitu/display
 180 insitu_display_url        /data/images/insitu/display
 181 insitu_input_dir          /data/prod/public/images/insitu/incoming
 182
 183 #path to our production_ftp site
 184 ftpsite_root              /data/prod/public
 185 ftpsite_url               ftp://ftp.solgenomics.net
 186
 187 #path to the pucebaboon temperature sensor file:
 188 pucebaboon_file        /data/prod/public/digitemp.out