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 ### Cview configuration parameters
  56 <Controller::Cview>
  57         cview_default_map_id 9
  58 </Controller::Cview>
  59
  60 ### backcompat variables for the various static content types
  61 # relative URL and absolute path for static datasets
  62 static_datasets_url       /data
  63 static_datasets_path      /data/prod/public
  64
  65 # relative URL and absoluate path for static site content
  66 static_content_url        /static_content
  67 static_content_path       /data/prod/public/sgn_static_content
  68 homepage_files_dir        /data/prod/public/sgn_static_content/homepage
  69
  70 # this needs to be here rather than in the CGI controller itself to
  71 # work around a bug in all but the most recent
  72 # Catalyst::Controller::CGIBin
  73 <Controller::CGI>
  74     cgi_dir   __path_to(cgi-bin)__
  75 </Controller::CGI>
  76
  77 <View::Email::ErrorEmail>
  78     <default>
  79         content_type  text/plain
  80         to            sgn-bugs@solgenomics.net
  81         from          sgn-bugs@solgenomics.net
  82         charset       utf-8
  83     </default>
  84     dump_skip_class   Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet  DBIx::Class::Row
  85 </View::Email::ErrorEmail>
  86
  87 # should we send emails, if we are a production server? this can be
  88 # used to turn off emails if we are being bombarded.
  89 admin_email              sgn-feedback@solgenomics.net
  90 feedback_email           sgn-feedback@solgenomics.net
  91 bugs_email               sgn-bugs@solgenomics.net
  92 email                    sgn-feedback@solgenomics.net
  93 disable_emails           0
  94
  95 # URL of the cnaonical, main production site
  96 main_production_site_url  http://solgenomics.net
  97
  98 #is there a system message text file somewhere we should be displaying?
  99 system_message_file
 100 # defaults to /tmp/<user>/SGN-site
 101 tempfiles_base
 102
 103 #R qtl tempfiles (must be cluster accessible)
 104 r_qtl_temp_path           /data/prod/tmp/r_qtl___USERNAME__
 105
 106 #allow people to log in?
 107 disable_login             0
 108
 109 # where to run cluster jobs
 110 web_cluster_queue
 111
 112 #is this a mirror of SGN, or the real thing?
 113 is_mirror                 0
 114
 115 # how to find cosii_files for markerinfo.pl
 116 cosii_files               /data/cosii2
 117
 118 # log files, ABSOLUTE PATHS
 119 error_log                 /var/log/sgn-site/error.log
 120 access_log                /var/log/sgn-site/access.log
 121 rewrite_log               /var/log/sgn-site/rewrite.log
 122
 123 # paths to stuff
 124 hmmsearch_location        hmmsearch
 125 intron_finder_database    /data/prod/public/intron_finder_database
 126
 127 trace_path                /data/prod/public/chromatograms
 128 image_dir                 /images/image_files
 129 image_path                /data/prod/public/images
 130 tempfiles_subdir          /static/documents/tempfiles
 131 submit_dir                /data/shared/submit-uploads
 132 programs_subdir           /programs
 133 documents_subdir          /documents
 134 conf_subdir               /conf
 135 support_data_subdir       /support_data
 136
 137 #currently our cookies encrypt stuff, so this is just a random string to use to do that
 138 cookie_encryption_key     bo9yie2JeeVee6ouAhch9aomeesieJ3iShae8aa8
 139
 140 # where the genefamily info is stored
 141 genefamily_dir            /data/prod/private/genomes/genefamily/
 142
 143 <feature SGN::Feature::FeaturePages>
 144     enabled      1
 145 </feature>
 146 <feature SGN::Feature::LocusPages>
 147     enabled      1
 148 </feature>
 149
 150 # default GBrowse2 configuration, for a Debian gbrowse2 installation
 151 <feature SGN::Feature::GBrowse2>
 152     enabled      1
 153     perl_inc     /usr/share/gbrowse/lib/perl5
 154     tmp_dir      /var/tmp/gbrowse
 155     cgi_url      /gbrowse/bin
 156     static_url   /gbrowse/static
 157     run_mode     fcgi
 158     cgi_bin      /usr/share/gbrowse/cgi-bin
 159     static_dir   /usr/share/gbrowse/htdocs
 160 </feature>
 161
 162 # default ITAG config
 163 <feature SGN::Feature::ITAG>
 164     enabled         1
 165     pipeline_base   /data/shared/tomato_genome/itagpipeline/itag
 166     releases_base   /data/prod/private/genomes/solanum_lycopersicum/annotation
 167 </feature>
 168
 169 cview_db_backend    cxgn
 170
 171 #how to find blast stuff
 172 blast_path                ""
 173 blast_db_path             /data/shared/blast/databases/current
 174
 175 #the shared temp directory used by cluster nodes
 176 cluster_shared_tempdir    /data/prod/tmp
 177
 178 #how verbose we want the warnings to be in the apache error log
 179 verbose_warnings          1
 180
 181 # Insitu file locations
 182 insitu_fullsize_dir       /data/prod/public/images/insitu/processed
 183 insitu_fullsize_url       /data/images/insitu/processed
 184 insitu_display_dir        /data/prod/public/images/insitu/display
 185 insitu_display_url        /data/images/insitu/display
 186 insitu_input_dir          /data/prod/public/images/insitu/incoming
 187
 188 #path to our production_ftp site
 189 ftpsite_root              /data/prod/public
 190 ftpsite_url               ftp://ftp.solgenomics.net
 191
 192 #path to the pucebaboon temperature sensor file:
 193 pucebaboon_file        /data/prod/public/digitemp.out