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 vigs_tool_blast_datasets 148 149 196 69
  14
  15 project_name SGN
  16
  17 disable_login 0
  18
  19 # who is the web server user for chowning and emailing.  need to set
  20 # these manually under Apache mod_perl for example, because the server
  21 # runs under a different user than when it starts.
  22 www_user                 __USERNAME__
  23 www_group                __GROUPNAME__
  24
  25 solgs_dir        /data/prod/tmp/solgs/__USERNAME__
  26
  27 # when true, server removes its tempfiles when the app is started
  28 clear_tempfiles_on_restart  1
  29
  30 r_qtl_temp_path /data/prod/tmp/solqtl___USERNAME__
  31
  32 ##### other config variables #####
  33
  34 dbsearchpath   sgn
  35 dbsearchpath   public
  36 dbsearchpath   annotation
  37 dbsearchpath   genomic
  38 dbsearchpath   insitu
  39 dbsearchpath   metadata
  40 dbsearchpath   pheno_population
  41 dbsearchpath   phenome
  42 dbsearchpath   physical
  43 dbsearchpath   tomato_gff
  44 dbsearchpath   biosource
  45 dbsearchpath   gem
  46
  47 <DatabaseConnection sgn_test>
  48         #password   set_this_please
  49         dsn   dbi:Pg:host=localhost;dbname=cxgn
  50         user   postgres
  51         search_path   public
  52         search_path   sgn
  53         search_path   annotation
  54         search_path   genomic
  55         search_path   insitu
  56         search_path   metadata
  57         search_path   pheno_population
  58         search_path   phenome
  59         search_path   physical
  60         search_path   tomato_gff
  61         search_path   biosource
  62         search_path   gem
  63 </DatabaseConnection>
  64
  65 ### Cview configuration parameters
  66 <Controller::Cview>
  67         cview_default_map_id 9
  68 </Controller::Cview>
  69
  70 ## captcha keys for the production site
  71 captcha_private_key  6Lc__9YSAAAAANcTczARhRnZRkKmzWjnhipyqI6f
  72 captcha_public_key   6Lc__9YSAAAAAH2ODL2FlR8jKa2Ms9i9d_0ziBWr
  73
  74 contact_form_human_question 2+3
  75 contact_form_human_answer   5
  76
  77 ### backcompat variables for the various static content types
  78 # relative URL and absolute path for static datasets
  79 static_datasets_url       /data
  80 static_datasets_path      /data/prod/public
  81
  82 # relative URL and absoluate path for static site content
  83 static_content_url        /static_content
  84 static_content_path       /data/prod/public/sgn_static_content
  85 homepage_files_dir        /data/prod/public/sgn_static_content/homepage
  86
  87 # this needs to be here rather than in the CGI controller itself to
  88 # work around a bug in all but the most recent
  89 # Catalyst::Controller::CGIBin
  90 <Controller::CGI>
  91     cgi_dir   __path_to(cgi-bin)__
  92 </Controller::CGI>
  93
  94 <Controller::Genomes::Tomato>
  95    bac_publish_subdir tomato_genome/bacs
  96 </Controller::Genomes::Tomato>
  97
  98 <View::Email::ErrorEmail>
  99     <default>
 100         content_type  text/plain
 101         to            sgn-bugs@solgenomics.net
 102         from          sgn-bugs@solgenomics.net
 103         charset       utf-8
 104     </default>
 105     dump_skip_class   Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet  DBIx::Class::Row  HTML::Mason::Interp
 106 </View::Email::ErrorEmail>
 107
 108 # should we send emails, if we are a production server? this can be
 109 # used to turn off emails if we are being bombarded.
 110 admin_email              sgn-feedback@solgenomics.net
 111 feedback_email           sgn-feedback@solgenomics.net
 112 bugs_email               sgn-bugs@solgenomics.net
 113 email                    sgn-feedback@solgenomics.net
 114 tokn_email               scp78@cornell.edu
 115 disable_emails           0
 116
 117 # URL of the canonical, main production site
 118 main_production_site_url  http://solgenomics.net
 119
 120 #is there a system message text file somewhere we should be displaying?
 121 system_message_file       __HOME__/system_message.txt
 122 # defaults to /tmp/<user>/SGN-site
 123 #tempfiles_base
 124
 125
 126 tempfiles_base            ""
 127 #
 128
 129 # where to run cluster jobs - nothing means "batch" queue
 130 #web_cluster_queue
 131
 132
 133 # where to run cluster jobs
 134 web_cluster_queue        batch
 135
 136
 137 #is this a mirror of SGN, or the real thing?
 138 is_mirror                 0
 139 #
 140 # how to find cosii_files for markerinfo.pl
 141 cosii_files               /data/cosii2
 142 #
 143 # log files, ABSOLUTE PATHS
 144 error_log                 /var/log/sgn-site/error.log
 145 access_log                /var/log/sgn-site/access.log
 146 rewrite_log               /var/log/sgn-site/rewrite.log
 147 #
 148 # paths to stuff
 149 hmmsearch_location        hmmsearch
 150 intron_finder_database    /data/prod/public/intron_finder_database
 151 #
 152 trace_path                /data/prod/public/chromatograms
 153 image_dir                 /images/image_files
 154 image_path                /data/prod/public/images
 155 tempfiles_subdir          /static/documents/tempfiles
 156 submit_dir                /data/shared/submit-uploads
 157 programs_subdir           /programs
 158 documents_subdir          /documents
 159 conf_subdir               /conf
 160 support_data_subdir       /support_data
 161 #
 162 #stock tempfiles (for downloading phenotype and genotype raw data)
 163 stock_tempfiles           /static/documents/tempfiles/stock
 164 #
 165 #currently our cookies encrypt stuff, so this is just a random string to use to do that
 166 cookie_encryption_key     bo9yie2JeeVee6ouAhch9aomeesieJ3iShae8aa8
 167 #
 168 # where the genefamily info is stored
 169 genefamily_dir            /data/prod/private/genomes/genefamily/
 170 #
 171 # the right ontology db name for the trait search
 172 trait_ontology_db_name SP
 173 onto_root_namespaces  GO (Gene Ontology), PO (Plant Ontology), SO (Sequence Ontology), PATO (Phenotype and Trait Ontology), SP (Solanaceae Ontology)
 174 ##
 175
 176 <feature SGN::Feature::FeaturePages>
 177     enabled      1
 178 </feature>
 179 <feature SGN::Feature::LocusPages>
 180     enabled      1
 181 </feature>
 182 #
 183 # default GBrowse2 configuration, for a Debian gbrowse2 installation
 184 <feature SGN::Feature::GBrowse2>
 185     enabled      1
 186     perl_inc     /usr/share/gbrowse/lib/perl5
 187     tmp_dir      /var/tmp/gbrowse
 188     cgi_url      /gbrowse/bin
 189     static_url   /gbrowse/static
 190     run_mode     fcgi
 191     cgi_bin      /usr/share/gbrowse/cgi-bin
 192     static_dir   /usr/share/gbrowse/htdocs
 193 </feature>
 194 #
 195 # default ITAG config
 196 <feature SGN::Feature::ITAG>
 197     enabled         1
 198     pipeline_base   /data/shared/tomato_genome/itagpipeline/itag
 199     releases_base   /data/prod/private/genomes/solanum_lycopersicum/annotation
 200 </feature>
 201 #
 202 cview_db_backend    cxgn
 203 #
 204 #how to find blast stuff
 205 blast_path                ""
 206 blast_db_path             /data/shared/blast/databases/current
 207
 208 vigs_tool_blast_datasets  148 149 196 69
 209 #
 210 #bin directory used by cluster nodes
 211 cluster_shared_bindir /data/prod/bin
 212 #
 213 #the shared temp directory used by cluster nodes
 214 cluster_shared_tempdir    /data/prod/tmp
 215 #
 216 #how verbose we want the warnings to be in the apache error log
 217 verbose_warnings          1
 218 #
 219 # Insitu file locations
 220 insitu_fullsize_dir       /data/prod/public/images/insitu/processed
 221 insitu_fullsize_url       /data/images/insitu/processed
 222 insitu_display_dir        /data/prod/public/images/insitu/display
 223 insitu_display_url        /data/images/insitu/display
 224 insitu_input_dir          /data/prod/public/images/insitu/incoming
 225 #
 226 #path to our production_ftp site
 227 ftpsite_root              /data/prod/public
 228 ftpsite_url               ftp://ftp.solgenomics.net
 229 #path to the pucebaboon temperature sensor file:
 230 pucebaboon_file        /data/prod/public/digitemp.out
 231 #
 232 #path for archving uploaded files
 233 archive_path     /data/prod/sgn_archive
 234
 235 #site overall identifier prefix used for site specific data
 236 #such as stocks, unignes (yet to be implemented) and other datatypes
 237 #for example, uploading barcode phenotyping data will not work without this key (see L<CXGN::Stock::StockBarcode> )
 238 identifier_prefix   SGN