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 rootpath /home/vagrant/cxgn
  14 basepath /home/vagrant/cxgn/sgn
  15
  16 composable_cvs trait,object,tod,toy,unit,method
  17 composable_cvs_allowed_combinations Agronomic|trait+toy,Metabolic|trait+object+tod+toy+unit+method
  18 composable_cvterm_delimiter |
  19 composable_cvterm_format concise
  20 composable_tod_root_cvterm "time of day|TIME:0000001"
  21 composable_toy_root_cvterm "time of year|TIME:0000005"
  22 composable_gen_root_cvterm "generation|TIME:0000072"
  23 allow_observation_variable_submission_interface 0
  24 trait_cv_name cassava_trait
  25 trait_ontology_db_name SP
  26 # For displaying ontologies in Ontology Browser
  27 onto_root_namespaces  GO (Gene Ontology), PO (Plant Ontology), SO (Sequence Ontology), PATO (Phenotype and Trait Ontology), SP (Solanaceae Ontology), UO (Units), CASSTISS (Cass tissues)
  28 # For Trait Search page
  29 trait_variable_onto_root_namespaces CO_322 (Cassava Ontology), UO (Units), CASSTISS (Cass tissues), COMP (Composed Variables)
  30
  31 project_name SGN
  32
  33 disable_login 0
  34
  35 # Cluster backend
  36 backend Slurm
  37
  38 # the species that should be preselected in a list of species
  39 #
  40 preferred_species
  41
  42 # who is the web server user for chowning and emailing.  need to set
  43 # these manually under Apache mod_perl for example, because the server
  44 # runs under a different user than when it starts.
  45 www_user                 __USERNAME__
  46 www_group                __GROUPNAME__
  47
  48 # when true, server removes its tempfiles when the app is started
  49 clear_tempfiles_on_restart  1
  50
  51 solqtl /export/prod/tmp/solqtl/__USERNAME__
  52 ##### other config variables #####
  53
  54 dbsearchpath   sgn
  55 dbsearchpath   public
  56 dbsearchpath   annotation
  57 dbsearchpath   genomic
  58 dbsearchpath   insitu
  59 dbsearchpath   metadata
  60 dbsearchpath   pheno_population
  61 dbsearchpath   phenome
  62 dbsearchpath   physical
  63 dbsearchpath   tomato_gff
  64 dbsearchpath   biosource
  65 dbsearchpath   gem
  66 dbsearchpath   sgn_people
  67
  68 <DatabaseConnection sgn_test>
  69         #password   set_this_please
  70         dsn   dbi:Pg:host=localhost;dbname=cxgn
  71         user   postgres
  72         search_path   public
  73         search_path   sgn
  74         search_path   annotation
  75         search_path   genomic
  76         search_path   insitu
  77         search_path   metadata
  78         search_path   pheno_population
  79         search_path   phenome
  80         search_path   physical
  81         search_path   tomato_gff
  82         search_path   biosource
  83         search_path   gem
  84         search_path   sgn_people
  85 </DatabaseConnection>
  86
  87 ### Cview configuration parameters
  88 <Controller::Cview>
  89         cview_default_map_id 9
  90 </Controller::Cview>
  91
  92 ##Github access token used for contact form posting of issues
  93 github_access_token NULL
  94
  95 ## captcha keys for the production site
  96 #captcha_private_key  6Lc__9YSAAAAANcTczARhRnZRkKmzWjnhipyqI6f
  97 #captcha_public_key   6Lc__9YSAAAAAH2ODL2FlR8jKa2Ms9i9d_0ziBWr
  98
  99 ### backcompat variables for the various static content types
 100 # relative URL and absolute path for static datasets
 101 static_datasets_url       /data
 102 static_datasets_path      /export/prod/public
 103
 104 # relative URL and absoluate path for static site content
 105 static_content_url        /static_content
 106 static_content_path       /export/prod/public/sgn_static_content
 107 homepage_files_dir        /export/prod/public/sgn_static_content/homepage
 108
 109 # this needs to be here rather than in the CGI controller itself to
 110 # work around a bug in all but the most recent
 111 # Catalyst::Controller::CGIBin
 112 <Controller::CGI>
 113     cgi_dir   __path_to(cgi-bin)__
 114 </Controller::CGI>
 115
 116 <Controller::Genomes::Tomato>
 117    bac_publish_subdir tomato_genome/bacs
 118 </Controller::Genomes::Tomato>
 119
 120 <Plugin::SmartURI>
 121                disposition host-header   # application-wide
 122                uri_class   URI::SmartURI # by default
 123 </Plugin::SmartURI>
 124
 125
 126 <View::Email::ErrorEmail>
 127     <default>
 128         content_type  text/plain
 129         to            sgn-bugs@solgenomics.net
 130         from          sgn-bugs@solgenomics.net
 131         charset       utf-8
 132     </default>
 133     dump_skip_class   Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet  DBIx::Class::Row  HTML::Mason::Interp
 134 </View::Email::ErrorEmail>
 135
 136 # should we send emails, if we are a production server? this can be
 137 # used to turn off emails if we are being bombarded.
 138 admin_email              sgn-feedback@solgenomics.net
 139 feedback_email           sgn-feedback@solgenomics.net
 140 bugs_email               sgn-bugs@solgenomics.net
 141 email                    sgn-feedback@solgenomics.net
 142 contact_form_email       contactform@solgenomics.net
 143 tokn_email               scp78@cornell.edu
 144 disable_emails           0
 145
 146 # URL of the canonical, main production site
 147 main_production_site_url  http://solgenomics.net
 148
 149 #is there a system message text file somewhere we should be displaying?
 150 system_message_file       __HOME__/system_message.txt
 151 # defaults to /tmp/<user>/SGN-site
 152 #tempfiles_base
 153
 154
 155 tempfiles_base            ""
 156 #
 157
 158 # where to run cluster jobs - nothing means "batch" queue
 159 #web_cluster_queue
 160
 161
 162 # where to run cluster jobs
 163 web_cluster_queue        batch
 164
 165
 166 #is this a mirror of SGN, or the real thing?
 167 is_mirror                 0
 168 #
 169 # how to find cosii_files for markerinfo.pl
 170 cosii_files               /export/cosii2
 171 #
 172 # log files, ABSOLUTE PATHS
 173 error_log                 /var/log/sgn-site/error.log
 174 access_log                /var/log/sgn-site/access.log
 175 rewrite_log               /var/log/sgn-site/rewrite.log
 176 blast_log                 /export/prod/tmp/blast/blast.log
 177 #
 178 # paths to stuff
 179 hmmsearch_location        hmmsearch
 180 intron_finder_database    /export/prod/public/intron_finder_database
 181 #
 182 trace_path                /export/prod/public/chromatograms
 183 image_dir                 /images/image_files
 184 image_path                /export/prod/public/images
 185 tempfiles_subdir          /static/documents/tempfiles
 186 submit_dir                /data/shared/submit-uploads
 187 programs_subdir           /programs
 188 documents_subdir          /documents
 189 conf_subdir               /conf
 190 support_data_subdir       /support_data
 191 #
 192 #stock tempfiles (for downloading phenotype and genotype raw data)
 193 stock_tempfiles           /static/documents/tempfiles/stock
 194 #
 195 #currently our cookies encrypt stuff, so this is just a random string to use to do that
 196 cookie_encryption_key     bo9yie2JeeVee6ouAhch9aomeesieJ3iShae8aa8
 197 #
 198 # where the genefamily info is stored
 199 genefamily_dir            /export/prod/private/genomes/genefamily/
 200 #
 201
 202 ##
 203 # stock properties that should be displayed and allowed to be edited in the "additional information" section
 204 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,location_code,ploidy_level,genome_structure,ncbi_taxonomy_id,transgenic,introgression_parent,introgression_backcross_parent,introgression_map_version,introgression_chromosome,introgression_start_position_bp,introgression_end_position_bp
 205 ##
 206
 207 ## Cross properties that should be displayed and allowed to be added to crosses on cross detail page.
 208 ## Cross properties for cassavabase
 209 cross_properties Tag Number,Pollination Date,Number of Bags,Number of Flowers,Number of Fruits,Number of Seeds
 210
 211 ##Cross properties for yambase
 212 ##cross_properties Number of Flowers,Pollination Date,Harvest Date,Number of Seeds Harvested,Days to Maturity,Seed Extraction Date,Number of Seeds Extracted,Number of Viable Seeds,Number of Nonviable Seeds, Days from Harvest to Extraction
 213
 214 ##Cross properties for musabase
 215 ##cross_properties First Pollination Date,Repeat Pollination Date,Harvest Date,Seed Extraction Date,Number of Seeds Extracted,Embryo Rescue Good Seeds,Embryo Rescue Bad Seeds,Embryo Rescue Total Seeds,Embryo Rescue Date,Subculture Date,Subcultures Count,Subcultures Multiplication Number,Rooting Date,Rooting Plantlet,Germinating After 2 Weeks Date,Active Germinating After 2 Weeks,Germinating Afte 8 Weeks Date,Active Germinating After 8 Weeks,Screenhouse Transfer Date,Hardening Date
 216
 217 <feature SGN::Feature::FeaturePages>
 218     enabled      1
 219 </feature>
 220 <feature SGN::Feature::LocusPages>
 221     enabled      1
 222 </feature>
 223 #
 224 # default GBrowse2 configuration, for a Debian gbrowse2 installation
 225 <feature SGN::Feature::GBrowse2>
 226     enabled      1
 227     perl_inc     /usr/local/share/website/gbrowse/lib/perl5
 228     tmp_dir      /usr/local/share/website/tmp/gbrowse
 229     cgi_url      /gbrowse/bin
 230     static_url   /gbrowse/static
 231     run_mode     fastcgi
 232     cgi_bin      /usr/lib/cgi-bin/gbrowse
 233     static_dir   /usr/local/share/website/gbrowse/htdocs
 234 </feature>
 235 #
 236 # default ITAG config
 237 <feature SGN::Feature::ITAG>
 238     enabled         1
 239     pipeline_base   /export/shared/tomato_genome/itagpipeline/itag
 240     releases_base   /export/prod/private/genomes/solanum_lycopersicum/annotation
 241 </feature>
 242 #
 243 cview_db_backend    cxgn
 244
 245 #how to find blast stuff
 246 blast_path                ""
 247 blast_db_path             /export/prod/blast/databases/current
 248 preselected_blastdb       224
 249 jbrowse_path              /jbrowse_solgenomics/?data=data/json
 250
 251
 252 #bin directory used by cluster nodes
 253 cluster_shared_bindir /export/prod/bin
 254 #
 255 #the shared temp directory used by cluster nodes
 256 cluster_shared_tempdir    /export/prod/tmp
 257 gbs_temp_data  /export/prod/public
 258
 259 #
 260 #how verbose we want the warnings to be in the apache error log
 261 verbose_warnings          1
 262 #
 263 # Insitu file locations
 264 insitu_fullsize_dir       /export/prod/public/images/insitu/processed
 265 insitu_fullsize_url       /export/images/insitu/processed
 266 insitu_display_dir        /export/prod/public/images/insitu/display
 267 insitu_display_url        /export/images/insitu/display
 268 insitu_input_dir          /export/prod/public/images/insitu/incoming
 269 #
 270 #path to our production_ftp site
 271 ftpsite_root              /export/prod/public
 272 ftpsite_url               ftp://ftp.solgenomics.net
 273 #path to the pucebaboon temperature sensor file:
 274 pucebaboon_file        /export/prod/public/digitemp.out
 275 #
 276 #path for archving uploaded files
 277 archive_path     /export/prod/sgn_archive
 278
 279 #site overall identifier prefix used for site specific data
 280 #such as stocks, unignes (yet to be implemented) and other datatypes
 281 #for example, uploading barcode phenotyping data will not work without this key (see L<CXGN::Stock::StockBarcode> )
 282 identifier_prefix   SGN
 283
 284 #default genotyping protocol to use:
 285 default_genotyping_protocol undefined(set this in sgn_local.conf)
 286
 287 genotyping_server_host NULL
 288 genotyping_server_username NULL
 289 genotyping_server_password NULL
 290 genotyping_server_token NULL
 291
 292 #HIDAP Shiny Server Support
 293 hidap_enabled    0
 294
 295 #BrAPI params
 296 supportedCrop    Cassava
 297 brapi_require_login 0
 298
 299 #Expression Atlas Connection
 300 has_expression_atlas    0
 301 expression_atlas_url    0
 302
 303 #Homepage controller customization
 304 homepage_display_phenotype_uploads 0
 305
 306 #ODK Services
 307 odk_crossing_data_service_name NULL
 308 odk_crossing_data_service_url https://ona.io
 309 odk_crossing_data_service_username ONAUSER
 310 odk_crossing_data_service_password ONAPASS
 311 odk_crossing_data_test_form_name NULL
 312 odk_crossing_data_separate_wishlist_by_location 0
 313 odk_phenotyping_data_service_name NULL
 314 odk_phenotyping_data_service_url https://bio.smap.com.au
 315 odk_phenotyping_data_service_username SMAPUSER
 316 odk_phenotyping_data_service_password SMAPPASS
 317 crontab_file NULL
 318 crontab_log_filepath NULL