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 composable_cvs trait,object,tod,toy,unit,method
  14 composable_cvs_allowed_combinations Agronomic|trait+toy,Metabolic|trait+object+tod+toy+unit+method
  15 composable_cvterm_delimiter |
  16 composable_cvterm_format concise
  17 composable_tod_root_cvterm "time of day|TIME:0000001"
  18 composable_toy_root_cvterm "time of year|TIME:0000005"
  19 composable_gen_root_cvterm "generation|TIME:0000072"
  20
  21 trait_cv_name cassava_trait
  22
  23 project_name SGN
  24
  25 disable_login 0
  26
  27 # the species that should be preselected in a list of species
  28 #
  29 preferred_species
  30
  31 # who is the web server user for chowning and emailing.  need to set
  32 # these manually under Apache mod_perl for example, because the server
  33 # runs under a different user than when it starts.
  34 www_user                 __USERNAME__
  35 www_group                __GROUPNAME__
  36
  37 # when true, server removes its tempfiles when the app is started
  38 clear_tempfiles_on_restart  1
  39
  40 solqtl /export/prod/tmp/solqtl/__USERNAME__
  41 ##### other config variables #####
  42
  43 dbsearchpath   sgn
  44 dbsearchpath   public
  45 dbsearchpath   annotation
  46 dbsearchpath   genomic
  47 dbsearchpath   insitu
  48 dbsearchpath   metadata
  49 dbsearchpath   pheno_population
  50 dbsearchpath   phenome
  51 dbsearchpath   physical
  52 dbsearchpath   tomato_gff
  53 dbsearchpath   biosource
  54 dbsearchpath   gem
  55 dbsearchpath   sgn_people
  56
  57 <DatabaseConnection sgn_test>
  58         #password   set_this_please
  59         dsn   dbi:Pg:host=localhost;dbname=cxgn
  60         user   postgres
  61         search_path   public
  62         search_path   sgn
  63         search_path   annotation
  64         search_path   genomic
  65         search_path   insitu
  66         search_path   metadata
  67         search_path   pheno_population
  68         search_path   phenome
  69         search_path   physical
  70         search_path   tomato_gff
  71         search_path   biosource
  72         search_path   gem
  73         search_path   sgn_people
  74 </DatabaseConnection>
  75
  76 ### Cview configuration parameters
  77 <Controller::Cview>
  78         cview_default_map_id 9
  79 </Controller::Cview>
  80
  81 ## captcha keys for the production site
  82 #captcha_private_key  6Lc__9YSAAAAANcTczARhRnZRkKmzWjnhipyqI6f
  83 #captcha_public_key   6Lc__9YSAAAAAH2ODL2FlR8jKa2Ms9i9d_0ziBWr
  84
  85 ### backcompat variables for the various static content types
  86 # relative URL and absolute path for static datasets
  87 static_datasets_url       /data
  88 static_datasets_path      /export/prod/public
  89
  90 # relative URL and absoluate path for static site content
  91 static_content_url        /static_content
  92 static_content_path       /export/prod/public/sgn_static_content
  93 homepage_files_dir        /export/prod/public/sgn_static_content/homepage
  94
  95 # this needs to be here rather than in the CGI controller itself to
  96 # work around a bug in all but the most recent
  97 # Catalyst::Controller::CGIBin
  98 <Controller::CGI>
  99     cgi_dir   __path_to(cgi-bin)__
 100 </Controller::CGI>
 101
 102 <Controller::Genomes::Tomato>
 103    bac_publish_subdir tomato_genome/bacs
 104 </Controller::Genomes::Tomato>
 105
 106 <Plugin::SmartURI>
 107                disposition host-header   # application-wide
 108                uri_class   URI::SmartURI # by default
 109 </Plugin::SmartURI>
 110
 111
 112 <View::Email::ErrorEmail>
 113     <default>
 114         content_type  text/plain
 115         to            sgn-bugs@solgenomics.net
 116         from          sgn-bugs@solgenomics.net
 117         charset       utf-8
 118     </default>
 119     dump_skip_class   Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet  DBIx::Class::Row  HTML::Mason::Interp
 120 </View::Email::ErrorEmail>
 121
 122 # should we send emails, if we are a production server? this can be
 123 # used to turn off emails if we are being bombarded.
 124 admin_email              sgn-feedback@solgenomics.net
 125 feedback_email           sgn-feedback@solgenomics.net
 126 bugs_email               sgn-bugs@solgenomics.net
 127 email                    sgn-feedback@solgenomics.net
 128 contact_form_email       contactform@solgenomics.net
 129 tokn_email               scp78@cornell.edu
 130 disable_emails           0
 131
 132 # URL of the canonical, main production site
 133 main_production_site_url  http://solgenomics.net
 134
 135 #is there a system message text file somewhere we should be displaying?
 136 system_message_file       __HOME__/system_message.txt
 137 # defaults to /tmp/<user>/SGN-site
 138 #tempfiles_base
 139
 140
 141 tempfiles_base            ""
 142 #
 143
 144 # where to run cluster jobs - nothing means "batch" queue
 145 #web_cluster_queue
 146
 147
 148 # where to run cluster jobs
 149 web_cluster_queue        batch
 150
 151
 152 #is this a mirror of SGN, or the real thing?
 153 is_mirror                 0
 154 #
 155 # how to find cosii_files for markerinfo.pl
 156 cosii_files               /export/cosii2
 157 #
 158 # log files, ABSOLUTE PATHS
 159 error_log                 /var/log/sgn-site/error.log
 160 access_log                /var/log/sgn-site/access.log
 161 rewrite_log               /var/log/sgn-site/rewrite.log
 162 blast_log                 /export/prod/tmp/blast/blast.log
 163 #
 164 # paths to stuff
 165 hmmsearch_location        hmmsearch
 166 intron_finder_database    /export/prod/public/intron_finder_database
 167 #
 168 trace_path                /export/prod/public/chromatograms
 169 image_dir                 /images/image_files
 170 image_path                /export/prod/public/images
 171 tempfiles_subdir          /static/documents/tempfiles
 172 submit_dir                /data/shared/submit-uploads
 173 programs_subdir           /programs
 174 documents_subdir          /documents
 175 conf_subdir               /conf
 176 support_data_subdir       /support_data
 177 #
 178 #stock tempfiles (for downloading phenotype and genotype raw data)
 179 stock_tempfiles           /static/documents/tempfiles/stock
 180 #
 181 #currently our cookies encrypt stuff, so this is just a random string to use to do that
 182 cookie_encryption_key     bo9yie2JeeVee6ouAhch9aomeesieJ3iShae8aa8
 183 #
 184 # where the genefamily info is stored
 185 genefamily_dir            /export/prod/private/genomes/genefamily/
 186 #
 187 # the right ontology db name for the trait search
 188 trait_ontology_db_name SP
 189 onto_root_namespaces  GO (Gene Ontology), PO (Plant Ontology), SO (Sequence Ontology), PATO (Phenotype and Trait Ontology), SP (Solanaceae Ontology)
 190 ##
 191
 192 ##
 193 # stock properties that should be displayed and allowed to be edited in the "additional information" section
 194 #editable_stock_props variety,donor,donor institute,country of origin,state,adaptation,notes
 195 editable_stock_props variety,donor,donor institute,donor PUI,country of origin,state,institute code,institute name,biological status of accession code,notes,accession number,PUI,seed source,type of germplasm storage code,acquisition date,organization
 196 ##
 197
 198 <feature SGN::Feature::FeaturePages>
 199     enabled      1
 200 </feature>
 201 <feature SGN::Feature::LocusPages>
 202     enabled      1
 203 </feature>
 204 #
 205 # default GBrowse2 configuration, for a Debian gbrowse2 installation
 206 <feature SGN::Feature::GBrowse2>
 207     enabled      1
 208     perl_inc     /usr/local/share/website/gbrowse/lib/perl5
 209     tmp_dir      /usr/local/share/website/tmp/gbrowse
 210     cgi_url      /gbrowse/bin
 211     static_url   /gbrowse/static
 212     run_mode     fastcgi
 213     cgi_bin      /usr/lib/cgi-bin/gbrowse
 214     static_dir   /usr/local/share/website/gbrowse/htdocs
 215 </feature>
 216 #
 217 # default ITAG config
 218 <feature SGN::Feature::ITAG>
 219     enabled         1
 220     pipeline_base   /export/shared/tomato_genome/itagpipeline/itag
 221     releases_base   /export/prod/private/genomes/solanum_lycopersicum/annotation
 222 </feature>
 223 #
 224 cview_db_backend    cxgn
 225
 226
 227 #how to find blast stuff
 228 blast_path                ""
 229 blast_db_path             /export/prod/blast/databases/current
 230 preselected_blastdb       224
 231 jbrowse_path              /jbrowse_solgenomics/?data=data/json
 232
 233
 234 #bin directory used by cluster nodes
 235 cluster_shared_bindir /export/prod/bin
 236 #
 237 #the shared temp directory used by cluster nodes
 238 cluster_shared_tempdir    /export/prod/tmp
 239 gbs_temp_data  /export/prod/public
 240
 241 #
 242 #how verbose we want the warnings to be in the apache error log
 243 verbose_warnings          1
 244 #
 245 # Insitu file locations
 246 insitu_fullsize_dir       /export/prod/public/images/insitu/processed
 247 insitu_fullsize_url       /export/images/insitu/processed
 248 insitu_display_dir        /export/prod/public/images/insitu/display
 249 insitu_display_url        /export/images/insitu/display
 250 insitu_input_dir          /export/prod/public/images/insitu/incoming
 251 #
 252 #path to our production_ftp site
 253 ftpsite_root              /export/prod/public
 254 ftpsite_url               ftp://ftp.solgenomics.net
 255 #path to the pucebaboon temperature sensor file:
 256 pucebaboon_file        /export/prod/public/digitemp.out
 257 #
 258 #path for archving uploaded files
 259 archive_path     /export/prod/sgn_archive
 260
 261 #site overall identifier prefix used for site specific data
 262 #such as stocks, unignes (yet to be implemented) and other datatypes
 263 #for example, uploading barcode phenotyping data will not work without this key (see L<CXGN::Stock::StockBarcode> )
 264 identifier_prefix   SGN
 265
 266 #default genotyping protocol to use:
 267 default_genotyping_protocol undefined(set this in sgn_local.conf)
 268
 269 #HIDAP Shiny Server Support
 270 hidap_enabled    0
 271
 272 #BrAPI params
 273 supportedCrop    Cassava
 274
 275 #Expression Atlas Connection
 276 has_expression_atlas    0
 277 expression_atlas_url    0
 278
 279 #Homepage controller customization
 280 homepage_display_phenotype_uploads 0
 281
 282 #ONA API Authentication (Used for ODK tablet application being developed by Trushar)
 283 ona_username ONAUSER
 284 ona_password ONAPASS