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 <Controller::Genomes::Tomato>
  78    bac_publish_subdir tomato_genome/bacs
  79 </Controller::Genomes::Tomato>
  80
  81 <View::Email::ErrorEmail>
  82     <default>
  83         content_type  text/plain
  84         to            sgn-bugs@solgenomics.net
  85         from          sgn-bugs@solgenomics.net
  86         charset       utf-8
  87     </default>
  88     dump_skip_class   Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet  DBIx::Class::Row  HTML::Mason::Interp
  89 </View::Email::ErrorEmail>
  90
  91 # should we send emails, if we are a production server? this can be
  92 # used to turn off emails if we are being bombarded.
  93 admin_email              sgn-feedback@solgenomics.net
  94 feedback_email           sgn-feedback@solgenomics.net
  95 bugs_email               sgn-bugs@solgenomics.net
  96 email                    sgn-feedback@solgenomics.net
  97 disable_emails           0
  98
  99 # URL of the canonical, main production site
 100 main_production_site_url  http://solgenomics.net
 101
 102 #is there a system message text file somewhere we should be displaying?
 103 system_message_file       __HOME__/system_message.txt
 104 # defaults to /tmp/<user>/SGN-site
 105 tempfiles_base
 106
 107 #R qtl tempfiles (must be cluster accessible)
 108 r_qtl_temp_path           /data/prod/tmp/r_qtl___USERNAME__
 109
 110 #allow people to log in?
 111 disable_login             0
 112
 113 # where to run cluster jobs
 114 web_cluster_queue
 115
 116 #is this a mirror of SGN, or the real thing?
 117 is_mirror                 0
 118
 119 # how to find cosii_files for markerinfo.pl
 120 cosii_files               /data/cosii2
 121
 122 # log files, ABSOLUTE PATHS
 123 error_log                 /var/log/sgn-site/error.log
 124 access_log                /var/log/sgn-site/access.log
 125 rewrite_log               /var/log/sgn-site/rewrite.log
 126
 127 # paths to stuff
 128 hmmsearch_location        hmmsearch
 129 intron_finder_database    /data/prod/public/intron_finder_database
 130
 131 trace_path                /data/prod/public/chromatograms
 132 image_dir                 /images/image_files
 133 image_path                /data/prod/public/images
 134 tempfiles_subdir          /static/documents/tempfiles
 135 submit_dir                /data/shared/submit-uploads
 136 programs_subdir           /programs
 137 documents_subdir          /documents
 138 conf_subdir               /conf
 139 support_data_subdir       /support_data
 140
 141 #currently our cookies encrypt stuff, so this is just a random string to use to do that
 142 cookie_encryption_key     bo9yie2JeeVee6ouAhch9aomeesieJ3iShae8aa8
 143
 144 # where the genefamily info is stored
 145 genefamily_dir            /data/prod/private/genomes/genefamily/
 146
 147 <feature SGN::Feature::FeaturePages>
 148     enabled      1
 149 </feature>
 150 <feature SGN::Feature::LocusPages>
 151     enabled      1
 152 </feature>
 153
 154 # default GBrowse2 configuration, for a Debian gbrowse2 installation
 155 <feature SGN::Feature::GBrowse2>
 156     enabled      1
 157     perl_inc     /usr/share/gbrowse/lib/perl5
 158     tmp_dir      /var/tmp/gbrowse
 159     cgi_url      /gbrowse/bin
 160     static_url   /gbrowse/static
 161     run_mode     fcgi
 162     cgi_bin      /usr/share/gbrowse/cgi-bin
 163     static_dir   /usr/share/gbrowse/htdocs
 164 </feature>
 165
 166 # default ITAG config
 167 <feature SGN::Feature::ITAG>
 168     enabled         1
 169     pipeline_base   /data/shared/tomato_genome/itagpipeline/itag
 170     releases_base   /data/prod/private/genomes/solanum_lycopersicum/annotation
 171 </feature>
 172
 173 cview_db_backend    cxgn
 174
 175 #how to find blast stuff
 176 blast_path                ""
 177 blast_db_path             /data/shared/blast/databases/current
 178
 179 #the shared temp directory used by cluster nodes
 180 cluster_shared_tempdir    /data/prod/tmp
 181
 182 #how verbose we want the warnings to be in the apache error log
 183 verbose_warnings          1
 184
 185 # Insitu file locations
 186 insitu_fullsize_dir       /data/prod/public/images/insitu/processed
 187 insitu_fullsize_url       /data/images/insitu/processed
 188 insitu_display_dir        /data/prod/public/images/insitu/display
 189 insitu_display_url        /data/images/insitu/display
 190 insitu_input_dir          /data/prod/public/images/insitu/incoming
 191
 192 #path to our production_ftp site
 193 ftpsite_root              /data/prod/public
 194 ftpsite_url               ftp://ftp.solgenomics.net
 195
 196 #path to the pucebaboon temperature sensor file:
 197 pucebaboon_file        /data/prod/public/digitemp.out