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