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 project_name SGN
  14
  15 disable_login 0
  16
  17 # who is the web server user for chowning and emailing.  need to set
  18 # these manually under Apache mod_perl for example, because the server
  19 # runs under a different user than when it starts.
  20 www_user                 __USERNAME__
  21 www_group                __GROUPNAME__
  22
  23 # when true, server removes its tempfiles when the app is started
  24 clear_tempfiles_on_restart  1
  25
  26 solqtl /export/prod/tmp/solqtl/__USERNAME__
  27 ##### other config variables #####
  28
  29 dbsearchpath   sgn
  30 dbsearchpath   public
  31 dbsearchpath   annotation
  32 dbsearchpath   genomic
  33 dbsearchpath   insitu
  34 dbsearchpath   metadata
  35 dbsearchpath   pheno_population
  36 dbsearchpath   phenome
  37 dbsearchpath   physical
  38 dbsearchpath   tomato_gff
  39 dbsearchpath   biosource
  40 dbsearchpath   gem
  41 dbsearchpath   sgn_people
  42
  43 <DatabaseConnection sgn_test>
  44         #password   set_this_please
  45         dsn   dbi:Pg:host=localhost;dbname=cxgn
  46         user   postgres
  47         search_path   public
  48         search_path   sgn
  49         search_path   annotation
  50         search_path   genomic
  51         search_path   insitu
  52         search_path   metadata
  53         search_path   pheno_population
  54         search_path   phenome
  55         search_path   physical
  56         search_path   tomato_gff
  57         search_path   biosource
  58         search_path   gem
  59         search_path   sgn_people
  60 </DatabaseConnection>
  61
  62 ### Cview configuration parameters
  63 <Controller::Cview>
  64         cview_default_map_id 9
  65 </Controller::Cview>
  66
  67 ## captcha keys for the production site
  68 captcha_private_key  6Lc__9YSAAAAANcTczARhRnZRkKmzWjnhipyqI6f
  69 captcha_public_key   6Lc__9YSAAAAAH2ODL2FlR8jKa2Ms9i9d_0ziBWr
  70
  71 contact_form_human_question 2+3
  72 contact_form_human_answer   5
  73
  74 ### backcompat variables for the various static content types
  75 # relative URL and absolute path for static datasets
  76 static_datasets_url       /data
  77 static_datasets_path      /export/prod/public
  78
  79 # relative URL and absoluate path for static site content
  80 static_content_url        /static_content
  81 static_content_path       /export/prod/public/sgn_static_content
  82 homepage_files_dir        /export/prod/public/sgn_static_content/homepage
  83
  84 # this needs to be here rather than in the CGI controller itself to
  85 # work around a bug in all but the most recent
  86 # Catalyst::Controller::CGIBin
  87 <Controller::CGI>
  88     cgi_dir   __path_to(cgi-bin)__
  89 </Controller::CGI>
  90
  91 <Controller::Genomes::Tomato>
  92    bac_publish_subdir tomato_genome/bacs
  93 </Controller::Genomes::Tomato>
  94
  95 <Plugin::SmartURI>
  96                disposition host-header   # application-wide
  97                uri_class   URI::SmartURI # by default
  98 </Plugin::SmartURI>
  99
 100
 101 <View::Email::ErrorEmail>
 102     <default>
 103         content_type  text/plain
 104         to            sgn-bugs@solgenomics.net
 105         from          sgn-bugs@solgenomics.net
 106         charset       utf-8
 107     </default>
 108     dump_skip_class   Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet  DBIx::Class::Row  HTML::Mason::Interp
 109 </View::Email::ErrorEmail>
 110
 111 # should we send emails, if we are a production server? this can be
 112 # used to turn off emails if we are being bombarded.
 113 admin_email              sgn-feedback@solgenomics.net
 114 feedback_email           sgn-feedback@solgenomics.net
 115 bugs_email               sgn-bugs@solgenomics.net
 116 email                    sgn-feedback@solgenomics.net
 117 contact_form_email       contactform@solgenomics.net
 118 tokn_email               scp78@cornell.edu
 119 disable_emails           0
 120
 121 # URL of the canonical, main production site
 122 main_production_site_url  http://solgenomics.net
 123
 124 #is there a system message text file somewhere we should be displaying?
 125 system_message_file       __HOME__/system_message.txt
 126 # defaults to /tmp/<user>/SGN-site
 127 #tempfiles_base
 128
 129
 130 tempfiles_base            ""
 131 #
 132
 133 # where to run cluster jobs - nothing means "batch" queue
 134 #web_cluster_queue
 135
 136
 137 # where to run cluster jobs
 138 web_cluster_queue        batch
 139
 140
 141 #is this a mirror of SGN, or the real thing?
 142 is_mirror                 0
 143 #
 144 # how to find cosii_files for markerinfo.pl
 145 cosii_files               /export/cosii2
 146 #
 147 # log files, ABSOLUTE PATHS
 148 error_log                 /var/log/sgn-site/error.log
 149 access_log                /var/log/sgn-site/access.log
 150 rewrite_log               /var/log/sgn-site/rewrite.log
 151 blast_log                 /export/prod/tmp/blast/blast.log
 152 #
 153 # paths to stuff
 154 hmmsearch_location        hmmsearch
 155 intron_finder_database    /export/prod/public/intron_finder_database
 156 #
 157 trace_path                /export/prod/public/chromatograms
 158 image_dir                 /images/image_files
 159 image_path                /export/prod/public/images
 160 tempfiles_subdir          /static/documents/tempfiles
 161 submit_dir                /data/shared/submit-uploads
 162 programs_subdir           /programs
 163 documents_subdir          /documents
 164 conf_subdir               /conf
 165 support_data_subdir       /support_data
 166 #
 167 #stock tempfiles (for downloading phenotype and genotype raw data)
 168 stock_tempfiles           /static/documents/tempfiles/stock
 169 #
 170 #currently our cookies encrypt stuff, so this is just a random string to use to do that
 171 cookie_encryption_key     bo9yie2JeeVee6ouAhch9aomeesieJ3iShae8aa8
 172 #
 173 # where the genefamily info is stored
 174 genefamily_dir            /export/prod/private/genomes/genefamily/
 175 #
 176 # the right ontology db name for the trait search
 177 trait_ontology_db_name SP
 178 onto_root_namespaces  GO (Gene Ontology), PO (Plant Ontology), SO (Sequence Ontology), PATO (Phenotype and Trait Ontology), SP (Solanaceae Ontology)
 179 ##
 180
 181 <feature SGN::Feature::FeaturePages>
 182     enabled      1
 183 </feature>
 184 <feature SGN::Feature::LocusPages>
 185     enabled      1
 186 </feature>
 187 #
 188 # default GBrowse2 configuration, for a Debian gbrowse2 installation
 189 <feature SGN::Feature::GBrowse2>
 190     enabled      1
 191     perl_inc     /usr/local/share/website/gbrowse/lib/perl5
 192     tmp_dir      /usr/local/share/website/tmp/gbrowse
 193     cgi_url      /gbrowse/bin
 194     static_url   /gbrowse/static
 195     run_mode     fastcgi
 196     cgi_bin      /usr/lib/cgi-bin/gbrowse
 197     static_dir   /usr/local/share/website/gbrowse/htdocs
 198 </feature>
 199 #
 200 # default ITAG config
 201 <feature SGN::Feature::ITAG>
 202     enabled         1
 203     pipeline_base   /export/shared/tomato_genome/itagpipeline/itag
 204     releases_base   /export/prod/private/genomes/solanum_lycopersicum/annotation
 205 </feature>
 206 #
 207 cview_db_backend    cxgn
 208 #
 209 #how to find blast stuff
 210 blast_path                ""
 211 blast_db_path             /export/prod/blast/databases/current
 212 preselected_blastdb       224
 213 #
 214 #bin directory used by cluster nodes
 215 cluster_shared_bindir /export/prod/bin
 216 #
 217 #the shared temp directory used by cluster nodes
 218 cluster_shared_tempdir    /export/prod/tmp
 219 gbs_temp_data  /export/prod/public
 220
 221 #
 222 #how verbose we want the warnings to be in the apache error log
 223 verbose_warnings          1
 224 #
 225 # Insitu file locations
 226 insitu_fullsize_dir       /export/prod/public/images/insitu/processed
 227 insitu_fullsize_url       /export/images/insitu/processed
 228 insitu_display_dir        /export/prod/public/images/insitu/display
 229 insitu_display_url        /export/images/insitu/display
 230 insitu_input_dir          /export/prod/public/images/insitu/incoming
 231 #
 232 #path to our production_ftp site
 233 ftpsite_root              /export/prod/public
 234 ftpsite_url               ftp://ftp.solgenomics.net
 235 #path to the pucebaboon temperature sensor file:
 236 pucebaboon_file        /export/prod/public/digitemp.out
 237 #
 238 #path for archving uploaded files
 239 archive_path     /export/prod/sgn_archive
 240
 241 #site overall identifier prefix used for site specific data
 242 #such as stocks, unignes (yet to be implemented) and other datatypes
 243 #for example, uploading barcode phenotyping data will not work without this key (see L<CXGN::Stock::StockBarcode> )
 244 identifier_prefix   SGN
 245
 246 #default genotyping protocol to use:
 247 default_genotyping_protocol undefined