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-test
  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 # when true, server removes its tempfiles when the app is started
  26 clear_tempfiles_on_restart  1
  27
  28 r_qtl_temp_path  /static/documents/tempfiles/solqtl/__USERNAME__
  29 ##### other config variables #####
  30
  31 dbsearchpath   sgn
  32 dbsearchpath   public
  33 dbsearchpath   annotation
  34 dbsearchpath   genomic
  35 dbsearchpath   insitu
  36 dbsearchpath   metadata
  37 dbsearchpath   pheno_population
  38 dbsearchpath   phenome
  39 dbsearchpath   physical
  40 dbsearchpath   tomato_gff
  41 dbsearchpath   biosource
  42 dbsearchpath   gem
  43 dbsearchpath   sgn_people
  44
  45 <DatabaseConnection sgn_test>
  46         #password   set_this_please
  47         dsn   dbi:Pg:host=localhost;dbname=cxgn
  48         user   postgres
  49         search_path   public
  50         search_path   sgn
  51         search_path   annotation
  52         search_path   genomic
  53         search_path   insitu
  54         search_path   metadata
  55         search_path   pheno_population
  56         search_path   phenome
  57         search_path   physical
  58         search_path   tomato_gff
  59         search_path   biosource
  60         search_path   gem
  61         search_path   sgn_people
  62 </DatabaseConnection>
  63
  64 ### Cview configuration parameters
  65 <Controller::Cview>
  66         cview_default_map_id 9
  67 </Controller::Cview>
  68
  69 ## captcha keys for the production site
  70 captcha_private_key  6Lc__9YSAAAAANcTczARhRnZRkKmzWjnhipyqI6f
  71 captcha_public_key   6Lc__9YSAAAAAH2ODL2FlR8jKa2Ms9i9d_0ziBWr
  72
  73 contact_form_human_question 2+3
  74 contact_form_human_answer   5
  75
  76 ### backcompat variables for the various static content types
  77 # relative URL and absolute path for static datasets
  78 static_datasets_url       /data
  79 static_datasets_path      /export/prod/public
  80
  81 # relative URL and absoluate path for static site content
  82 static_content_url        /static_content
  83 static_content_path       /export/prod/public/sgn_static_content
  84 homepage_files_dir        /export/prod/public/sgn_static_content/homepage
  85
  86 # this needs to be here rather than in the CGI controller itself to
  87 # work around a bug in all but the most recent
  88 # Catalyst::Controller::CGIBin
  89 <Controller::CGI>
  90     cgi_dir   __path_to(cgi-bin)__
  91 </Controller::CGI>
  92
  93 <Controller::Genomes::Tomato>
  94    bac_publish_subdir tomato_genome/bacs
  95 </Controller::Genomes::Tomato>
  96
  97 <Plugin::SmartURI>
  98                disposition host-header   # application-wide
  99                uri_class   URI::SmartURI # by default
 100 </Plugin::SmartURI>
 101
 102
 103 <View::Email::ErrorEmail>
 104     <default>
 105         content_type  text/plain
 106         to            sgn-bugs@solgenomics.net
 107         from          sgn-bugs@solgenomics.net
 108         charset       utf-8
 109     </default>
 110     dump_skip_class   Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet  DBIx::Class::Row  HTML::Mason::Interp
 111 </View::Email::ErrorEmail>
 112
 113 # should we send emails, if we are a production server? this can be
 114 # used to turn off emails if we are being bombarded.
 115 admin_email              sgn-feedback@solgenomics.net
 116 feedback_email           sgn-feedback@solgenomics.net
 117 bugs_email               sgn-bugs@solgenomics.net
 118 email                    sgn-feedback@solgenomics.net
 119 tokn_email               scp78@cornell.edu
 120 disable_emails           0
 121
 122 # URL of the canonical, main production site
 123 main_production_site_url  http://solgenomics.net
 124
 125 #is there a system message text file somewhere we should be displaying?
 126 system_message_file       __HOME__/system_message.txt
 127 # defaults to /tmp/<user>/SGN-site
 128 #tempfiles_base
 129
 130
 131 tempfiles_base            ""
 132 #
 133
 134 # where to run cluster jobs - nothing means "batch" queue
 135 #web_cluster_queue
 136
 137
 138 # where to run cluster jobs
 139 web_cluster_queue        batch
 140
 141
 142 #is this a mirror of SGN, or the real thing?
 143 is_mirror                 0
 144 #
 145 # how to find cosii_files for markerinfo.pl
 146 cosii_files               /export/cosii2
 147 #
 148 # log files, ABSOLUTE PATHS
 149 error_log                 /var/log/sgn-site/error.log
 150 access_log                /var/log/sgn-site/access.log
 151 rewrite_log               /var/log/sgn-site/rewrite.log
 152 blast_log                 /export/prod/tmp/blast/blast.log
 153 #
 154 # paths to stuff
 155 hmmsearch_location        hmmsearch
 156 intron_finder_database    /export/prod/public/intron_finder_database
 157 #
 158 trace_path                /export/prod/public/chromatograms
 159 image_dir                 /images/image_files
 160 image_path                /export/prod/public/images
 161 tempfiles_subdir          /static/documents/tempfiles
 162 submit_dir                /data/shared/submit-uploads
 163 programs_subdir           /programs
 164 documents_subdir          /documents
 165 conf_subdir               /conf
 166 support_data_subdir       /support_data
 167 #
 168 #stock tempfiles (for downloading phenotype and genotype raw data)
 169 stock_tempfiles           /static/documents/tempfiles/stock
 170 #
 171 #currently our cookies encrypt stuff, so this is just a random string to use to do that
 172 cookie_encryption_key     bo9yie2JeeVee6ouAhch9aomeesieJ3iShae8aa8
 173 #
 174 # where the genefamily info is stored
 175 genefamily_dir            /export/prod/private/genomes/genefamily/
 176 #
 177 # the right ontology db name for the trait search
 178 trait_ontology_db_name SP
 179 onto_root_namespaces  GO (Gene Ontology), PO (Plant Ontology), SO (Sequence Ontology), PATO (Phenotype and Trait Ontology), SP (Solanaceae Ontology)
 180 ##
 181
 182 <feature SGN::Feature::FeaturePages>
 183     enabled      1
 184 </feature>
 185 <feature SGN::Feature::LocusPages>
 186     enabled      1
 187 </feature>
 188 #
 189 # default GBrowse2 configuration, for a Debian gbrowse2 installation
 190 <feature SGN::Feature::GBrowse2>
 191     enabled      1
 192     perl_inc     /usr/local/share/website/gbrowse/lib/perl5
 193     tmp_dir      /usr/local/share/website/tmp/gbrowse
 194     cgi_url      /gbrowse/bin
 195     static_url   /gbrowse/static
 196     run_mode     fastcgi
 197     cgi_bin      /usr/lib/cgi-bin/gbrowse
 198     static_dir   /usr/local/share/website/gbrowse/htdocs
 199 </feature>
 200 #
 201 # default ITAG config
 202 <feature SGN::Feature::ITAG>
 203     enabled         1
 204     pipeline_base   /export/shared/tomato_genome/itagpipeline/itag
 205     releases_base   /export/prod/private/genomes/solanum_lycopersicum/annotation
 206 </feature>
 207 #
 208 cview_db_backend    cxgn
 209 #
 210 #how to find blast stuff
 211 blast_path                ""
 212 blast_db_path             /export/prod/blast/databases/current
 213
 214 vigs_tool_blast_datasets  148 149 196 69
 215 #
 216 #bin directory used by cluster nodes
 217 cluster_shared_bindir /export/prod/bin
 218 #
 219 #the shared temp directory used by cluster nodes
 220 cluster_shared_tempdir    /export/prod/tmp
 221 gbs_temp_data  /export/prod/public
 222
 223 #
 224 #how verbose we want the warnings to be in the apache error log
 225 verbose_warnings          1
 226 #
 227 # Insitu file locations
 228 insitu_fullsize_dir       /export/prod/public/images/insitu/processed
 229 insitu_fullsize_url       /export/images/insitu/processed
 230 insitu_display_dir        /export/prod/public/images/insitu/display
 231 insitu_display_url        /export/images/insitu/display
 232 insitu_input_dir          /export/prod/public/images/insitu/incoming
 233 #
 234 #path to our production_ftp site
 235 ftpsite_root              /export/prod/public
 236 ftpsite_url               ftp://ftp.solgenomics.net
 237 #path to the pucebaboon temperature sensor file:
 238 pucebaboon_file        /export/prod/public/digitemp.out
 239 #
 240 #path for archving uploaded files
 241 archive_path     /export/prod/sgn_archive
 242
 243 #site overall identifier prefix used for site specific data
 244 #such as stocks, unignes (yet to be implemented) and other datatypes
 245 #for example, uploading barcode phenotyping data will not work without this key (see L<CXGN::Stock::StockBarcode> )
 246 identifier_prefix   SGN