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 project_name SGN
  14
  15 # who is the web server user for chowning and emailing.  need to set
  16 # these manually under Apache mod_perl for example, because the server
  17 # runs under a different user than when it starts.
  18 www_user                 __USERNAME__
  19 www_group                __GROUPNAME__
  20
  21 # when true, server removes its tempfiles when the app is started
  22 clear_tempfiles_on_restart  1
  23
  24 ##### other config variables #####
  25
  26 dbsearchpath   sgn
  27 dbsearchpath   public
  28 dbsearchpath   annotation
  29 dbsearchpath   genomic
  30 dbsearchpath   insitu
  31 dbsearchpath   metadata
  32 dbsearchpath   pheno_population
  33 dbsearchpath   phenome
  34 dbsearchpath   physical
  35 dbsearchpath   tomato_gff
  36 dbsearchpath   biosource
  37 dbsearchpath   gem
  38
  39 <DatabaseConnection sgn_test>
  40         #password   set_this_please
  41         dsn   dbi:Pg:host=localhost;dbname=cxgn
  42         user   postgres
  43         search_path   public
  44         search_path   sgn
  45         search_path   annotation
  46         search_path   genomic
  47         search_path   insitu
  48         search_path   metadata
  49         search_path   pheno_population
  50         search_path   phenome
  51         search_path   physical
  52         search_path   tomato_gff
  53         search_path   biosource
  54         search_path   gem
  55 </DatabaseConnection>
  56
  57 ### Cview configuration parameters
  58 <Controller::Cview>
  59         cview_default_map_id 9
  60 </Controller::Cview>
  61
  62 ### backcompat variables for the various static content types
  63 # relative URL and absolute path for static datasets
  64 static_datasets_url       /data
  65 static_datasets_path      /data/prod/public
  66
  67 # relative URL and absoluate path for static site content
  68 static_content_url        /static_content
  69 static_content_path       /data/prod/public/sgn_static_content
  70 homepage_files_dir        /data/prod/public/sgn_static_content/homepage
  71
  72 # this needs to be here rather than in the CGI controller itself to
  73 # work around a bug in all but the most recent
  74 # Catalyst::Controller::CGIBin
  75 <Controller::CGI>
  76     cgi_dir   __path_to(cgi-bin)__
  77 </Controller::CGI>
  78
  79 <Controller::Genomes::Tomato>
  80    bac_publish_subdir tomato_genome/bacs
  81 </Controller::Genomes::Tomato>
  82
  83 <View::Email::ErrorEmail>
  84     <default>
  85         content_type  text/plain
  86         to            sgn-bugs@solgenomics.net
  87         from          sgn-bugs@solgenomics.net
  88         charset       utf-8
  89     </default>
  90     dump_skip_class   Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet  DBIx::Class::Row  HTML::Mason::Interp
  91 </View::Email::ErrorEmail>
  92
  93 # should we send emails, if we are a production server? this can be
  94 # used to turn off emails if we are being bombarded.
  95 admin_email              sgn-feedback@solgenomics.net
  96 feedback_email           sgn-feedback@solgenomics.net
  97 bugs_email               sgn-bugs@solgenomics.net
  98 email                    sgn-feedback@solgenomics.net
  99 disable_emails           0
 100
 101 # URL of the canonical, main production site
 102 main_production_site_url  http://solgenomics.net
 103
 104 #is there a system message text file somewhere we should be displaying?
 105 system_message_file       __HOME__/system_message.txt
 106 # defaults to /tmp/<user>/SGN-site
 107 tempfiles_base
 108
 109 #R qtl tempfiles (must be cluster accessible)
 110 r_qtl_temp_path           /data/prod/tmp/r_qtl___USERNAME__
 111
 112 #allow people to log in?
 113 disable_login             0
 114
 115 # where to run cluster jobs
 116 web_cluster_queue
 117
 118 #is this a mirror of SGN, or the real thing?
 119 is_mirror                 0
 120
 121 # how to find cosii_files for markerinfo.pl
 122 cosii_files               /data/cosii2
 123
 124 # log files, ABSOLUTE PATHS
 125 error_log                 /var/log/sgn-site/error.log
 126 access_log                /var/log/sgn-site/access.log
 127 rewrite_log               /var/log/sgn-site/rewrite.log
 128
 129 # paths to stuff
 130 hmmsearch_location        hmmsearch
 131 intron_finder_database    /data/prod/public/intron_finder_database
 132
 133 trace_path                /data/prod/public/chromatograms
 134 image_dir                 /images/image_files
 135 image_path                /data/prod/public/images
 136 tempfiles_subdir          /static/documents/tempfiles
 137 submit_dir                /data/shared/submit-uploads
 138 programs_subdir           /programs
 139 documents_subdir          /documents
 140 conf_subdir               /conf
 141 support_data_subdir       /support_data
 142
 143 #currently our cookies encrypt stuff, so this is just a random string to use to do that
 144 cookie_encryption_key     bo9yie2JeeVee6ouAhch9aomeesieJ3iShae8aa8
 145
 146 # where the genefamily info is stored
 147 genefamily_dir            /data/prod/private/genomes/genefamily/
 148
 149 <feature SGN::Feature::FeaturePages>
 150     enabled      1
 151 </feature>
 152 <feature SGN::Feature::LocusPages>
 153     enabled      1
 154 </feature>
 155
 156 # default GBrowse2 configuration, for a Debian gbrowse2 installation
 157 <feature SGN::Feature::GBrowse2>
 158     enabled      1
 159     perl_inc     /usr/share/gbrowse/lib/perl5
 160     tmp_dir      /var/tmp/gbrowse
 161     cgi_url      /gbrowse/bin
 162     static_url   /gbrowse/static
 163     run_mode     fcgi
 164     cgi_bin      /usr/share/gbrowse/cgi-bin
 165     static_dir   /usr/share/gbrowse/htdocs
 166 </feature>
 167
 168 # default ITAG config
 169 <feature SGN::Feature::ITAG>
 170     enabled         1
 171     pipeline_base   /data/shared/tomato_genome/itagpipeline/itag
 172     releases_base   /data/prod/private/genomes/solanum_lycopersicum/annotation
 173 </feature>
 174
 175 cview_db_backend    cxgn
 176
 177 #how to find blast stuff
 178 blast_path                ""
 179 blast_db_path             /data/shared/blast/databases/current
 180
 181 #the shared temp directory used by cluster nodes
 182 cluster_shared_tempdir    /data/prod/tmp
 183
 184 #how verbose we want the warnings to be in the apache error log
 185 verbose_warnings          1
 186
 187 # Insitu file locations
 188 insitu_fullsize_dir       /data/prod/public/images/insitu/processed
 189 insitu_fullsize_url       /data/images/insitu/processed
 190 insitu_display_dir        /data/prod/public/images/insitu/display
 191 insitu_display_url        /data/images/insitu/display
 192 insitu_input_dir          /data/prod/public/images/insitu/incoming
 193
 194 #path to our production_ftp site
 195 ftpsite_root              /data/prod/public
 196 ftpsite_url               ftp://ftp.solgenomics.net
 197
 198 #path to the pucebaboon temperature sensor file:
 199 pucebaboon_file        /data/prod/public/digitemp.out