sgn.conf

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