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