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   localhost
   9 dbname   fixture
  10 dbuser   web_usr
  11 #dbpass   set_this_here
  12
  13 rootpath /home/vagrant/cxgn
  14 basepath /home/vagrant/cxgn/sgn
  15
  16 show_transplanting_date 0
  17
  18 python_executable /home/vagrant/.virtualenvs/cv/bin/python3.5
  19 python_executable_maskrcnn_env /home/vagrant/.virtualenvs/cv/bin/python3.5
  20
  21 composable_cvs trait,object,tod,toy,unit,method
  22 composable_cvs_allowed_combinations Agronomic|trait+toy,Metabolic|trait+object+tod+toy+unit+method
  23 composable_cvterm_delimiter |
  24 composable_cvterm_format concise
  25 composable_tod_root_cvterm "time of day|TIME:0000001"
  26 composable_toy_root_cvterm "time of year|TIME:0000005"
  27 composable_gen_root_cvterm "generation|TIME:0000072"
  28 composable_evt_root_cvterm "event|TIME:0000477"
  29 composable_validation_check_name 0
  30 allow_observation_variable_submission_interface 0
  31 trait_ontology_db_name SP
  32 trait_ontology_cv_name solanaceae_trait
  33 trait_ontology_cvterm_name Solanaceae trait ontology
  34 # For displaying ontologies in Ontology Browser
  35 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)
  36
  37 # Seedlot Maintenance Events
  38 #
  39 # seedlot_maintenance_event_ontology_root
  40 # The DB:Accession of the root term of the ontology used to define the Seedlot Maintenance categories, events, and values
  41 # seedlot_maintenance_event_ontology_root SEEDLOT_MAINTENANCE:0000000
  42 seedlot_maintenance_event_ontology_root
  43 #
  44 # seedlot_maintenance_info_cvterms
  45 # The cvterm_id(s) of event(s) displayed as seedlot information on the record page
  46 # seedlot_maintenance_info_cvterms 78211,78168
  47 seedlot_maintenance_info_cvterms
  48
  49 project_name SGN
  50
  51 user_registration_join_breeding_programs 0  # when enabled, a new user can choose which breeding programs to join during registration
  52 user_registration_admin_confirmation 0      # when enabled, the new user confirmation message will be sent to the address(es) below instead of the user
  53 user_registration_admin_confirmation_email  # a comma-separated list of email addresses to send new user confirmation messages to, when the above is enabled
  54 disable_login 0
  55 default_login_janedoe 0
  56 require_login 0
  57
  58 brapi_require_login 0
  59 brapi_observation_units_require_login 1
  60 brapi_observations_require_login 1
  61 brapi_post_variables 0
  62 brapi_put_variables  0
  63 brapi_images_require_login 1
  64 brapi_variables_require_login 1
  65 brapi_lists_require_login 1
  66 #brapi_default_user admin
  67 #brapi_default_user_role curator
  68 # temporary feature flag until breedbase is storing treatments properly through brapi
  69 brapi_treatments_no_management_factor 1
  70 brapi_GET any
  71 brapi_POST submitter,curator
  72 brapi_PUT submitter,curator
  73 brapi_OPTIONS any
  74 brapi_include_CO_xref 1
  75 brapi_ou_order_plot_num 0
  76
  77 allow_repeat_measures 0
  78
  79 #export trait names as synonyms (1) or the original trait name (0)
  80 fieldbook_trait_synonym 1
  81
  82 list_trait_require_id 1
  83
  84 # Cluster backend
  85 backend Slurm
  86
  87 # crossing prediction tool - should the sex of the plants be taken into account? (for diecieous plants such as Yam)
  88 # if yes, provide the name of the variable that is used to score the sex of the plant
  89 #
  90 plant_sex_variable_name  "Plant sex estimation 0-4"
  91
  92 # the species that should be preselected in a list of species
  93 #
  94 preferred_species
  95
  96 # who is the web server user for chowning and emailing.  need to set
  97 # these manually under Apache mod_perl for example, because the server
  98 # runs under a different user than when it starts.
  99 www_user                 __USERNAME__
 100 www_group                __GROUPNAME__
 101
 102 # when true, server removes its tempfiles when the app is started
 103 clear_tempfiles_on_restart  1
 104
 105 show_grafting_interface 0
 106 graft_separator_string "_on_"
 107
 108 solqtl /export/prod/tmp/solqtl/__USERNAME__
 109 ##### other config variables #####
 110
 111 dbsearchpath   sgn
 112 dbsearchpath   public
 113 dbsearchpath   annotation
 114 dbsearchpath   genomic
 115 dbsearchpath   insitu
 116 dbsearchpath   metadata
 117 dbsearchpath   pheno_population
 118 dbsearchpath   phenome
 119 dbsearchpath   physical
 120 dbsearchpath   tomato_gff
 121 dbsearchpath   biosource
 122 dbsearchpath   gem
 123 dbsearchpath   sgn_people
 124
 125 <DatabaseConnection sgn_test>
 126         #password   set_this_please
 127         dsn   dbi:Pg:host=localhost;dbname=cxgn
 128         user   postgres
 129         search_path   public
 130         search_path   sgn
 131         search_path   annotation
 132         search_path   genomic
 133         search_path   insitu
 134         search_path   metadata
 135         search_path   pheno_population
 136         search_path   phenome
 137         search_path   physical
 138         search_path   tomato_gff
 139         search_path   biosource
 140         search_path   gem
 141         search_path   sgn_people
 142 </DatabaseConnection>
 143
 144 ### Cview configuration parameters
 145 <Controller::Cview>
 146         cview_default_map_id 9
 147 </Controller::Cview>
 148
 149 ##Github access token used for contact form posting of issues
 150 github_access_token NULL
 151
 152 ##NOAA National Climatic Data Center Access token
 153 noaa_ncdc_access_token NULL
 154
 155 ## captcha keys for the production site
 156 #captcha_private_key  6Lc__9YSAAAAANcTczARhRnZRkKmzWjnhipyqI6f
 157 #captcha_public_key   6Lc__9YSAAAAAH2ODL2FlR8jKa2Ms9i9d_0ziBWr
 158
 159 ### backcompat variables for the various static content types
 160 # relative URL and absolute path for static datasets
 161 static_datasets_url       /data
 162 static_datasets_path      /export/prod/public
 163
 164 # relative URL and absoluate path for static site content
 165 static_content_url        /static_content
 166 static_content_path       /export/prod/public/sgn_static_content
 167 homepage_files_dir        /export/prod/public/sgn_static_content/homepage
 168
 169 # this needs to be here rather than in the CGI controller itself to
 170 # work around a bug in all but the most recent
 171 # Catalyst::Controller::CGIBin
 172 <Controller::CGI>
 173     cgi_dir   __path_to(cgi-bin)__
 174 </Controller::CGI>
 175
 176 <Controller::Genomes::Tomato>
 177    bac_publish_subdir tomato_genome/bacs
 178 </Controller::Genomes::Tomato>
 179
 180 <Plugin::SmartURI>
 181                disposition host-header   # application-wide
 182                uri_class   URI::SmartURI # by default
 183 </Plugin::SmartURI>
 184
 185
 186 <View::Email::ErrorEmail>
 187     <default>
 188         content_type  text/plain
 189         to            sgn-bugs@solgenomics.net
 190         from          sgn-bugs@solgenomics.net
 191         charset       utf-8
 192     </default>
 193     dump_skip_class   Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet  DBIx::Class::Row  HTML::Mason::Interp
 194 </View::Email::ErrorEmail>
 195
 196 # should we send emails, if we are a production server? this can be
 197 # used to turn off emails if we are being bombarded.
 198 admin_email              sgn-feedback@solgenomics.net
 199 feedback_email           sgn-feedback@solgenomics.net
 200 bugs_email               sgn-bugs@solgenomics.net
 201 email                    sgn-feedback@solgenomics.net
 202 contact_form_email       contactform@solgenomics.net
 203 cluster_job_email        cluster-jobs@solgenomics.net
 204 tokn_email               scp78@cornell.edu
 205 disable_emails           0
 206
 207 # External SMTP Server to send emails
 208 smtp_server
 209 smtp_layer  ssl
 210 smtp_auth   AUTO
 211 smtp_port
 212 smtp_login
 213 smtp_pass
 214 smtp_from
 215
 216 # URL of the canonical, main production site
 217 main_production_site_url  http://solgenomics.net
 218
 219 #is there a system message text file somewhere we should be displaying?
 220 system_message_file       __HOME__/system_message.txt
 221 # defaults to /tmp/<user>/SGN-site
 222 #tempfiles_base
 223
 224
 225 tempfiles_base            ""
 226 #
 227
 228 # where to run cluster jobs - nothing means "batch" queue
 229 #web_cluster_queue
 230
 231
 232 # where to run cluster jobs
 233 web_cluster_queue        batch
 234
 235
 236 #is this a mirror of SGN, or the real thing?
 237 is_mirror                 0
 238 #
 239 # how to find cosii_files for markerinfo.pl
 240 cosii_files               /export/cosii2
 241 #
 242 # log files, ABSOLUTE PATHS
 243 error_log                 /var/log/sgn-site/error.log
 244 access_log                /var/log/sgn-site/access.log
 245 rewrite_log               /var/log/sgn-site/rewrite.log
 246 blast_log                 /export/prod/tmp/blast/blast.log
 247 image_analysis_log        /tmp/image_analysis.log
 248
 249 #
 250 # paths to stuff
 251 hmmsearch_location        hmmsearch
 252 intron_finder_database    /export/prod/public/intron_finder_database
 253 #
 254 trace_path                /export/prod/public/chromatograms
 255 image_dir                 /images/image_files
 256 image_path                /export/prod/public/images
 257 tempfiles_subdir          /static/documents/tempfiles
 258 submit_dir                /data/shared/submit-uploads
 259 programs_subdir           /programs
 260 documents_subdir          /documents
 261 conf_subdir               /conf
 262 support_data_subdir       /support_data
 263 #
 264 #stock tempfiles (for downloading phenotype and genotype raw data)
 265 stock_tempfiles           /static/documents/tempfiles/stock
 266 #weblogo tempfiles for motifs finder tools
 267 tmp_weblogo_path          /static/documents/tempfiles/
 268 #
 269 #currently our cookies encrypt stuff, so this is just a random string to use to do that
 270 cookie_encryption_key     bo9yie2JeeVee6ouAhch9aomeesieJ3iShae8aa8
 271 #
 272 # where the genefamily info is stored
 273 genefamily_dir            /export/prod/private/genomes/genefamily/
 274 #
 275
 276 ##
 277 # stock properties that should be displayed and allowed to be edited in the "additional information" section and can be used in the accession file upload
 278 editable_stock_props variety,released_variety_name,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
 279
 280 editable_stock_props_definitions released_variety_name:offical variety name of the accession or stock,location_code:location code(s) for the accession,ploidy:a number(s) indicating the ploidy (e.g. 2 for diploid or 3 for triploid),genome_structure:genome structure(s) for accession which take into account ploidy and ancestral genome info e.g. AAA or AB,variety:variety(s) can be defined as a group of individuals or plants having similar traits that can be reproduced true to type from generation to generation,donor:the accession_name(s) of the donor accession and should be used in conjunction with donor institute and donor PUI,donor institute:the institute(s) of the donor accession(s),donor PUI:the permanent unique identifier(s) of the donor accession,country of origin:the country(s) of origin,state:the state(s) of origin,institute code: the institute code(s) of origin,institute name:the institute name(s) of origin,biological status of accession code:code(s) indicating the state of accession,notes:free text for notes,accession number:accession number(s) for accession from germplasm bank,PUI:permanent unique identifier(s) of the accession,seed source:origin(s) of seed source,type of germplasm storage code:code(s) indicating the type of germplasm storage,acquisition date:date(s) of acquisition YYYYMMDD for accession,transgenic:indicates if accession is transgenic. Please indicate 1 if transgenic and empty if otherwise.,introgression_parent:if the accession you are adding has an introgression that originated from one of the parents you can specify the parent here,introgression_backcross_parent:the backcross parent for introducing an introgression into the accession being added,introgression_map_version:the map version for identifying the start and stop position of the introgression. e.g. AGPv2,introgression_chromosome:the chromosome number that the introgression is on,introgression_start_position_bp:the start position of the introgression in base pairs,introgression_end_position_bp:the end position of the introgression in base pairs
 281
 282 editable_vector_props Strain,CloningOrganism,InherentMarker,Backbone,SelectionMarker,CassetteName,VectorType,Gene,Promotors,Terminators
 283
 284 ##
 285
 286 ## Cross properties that should be displayed and allowed to be added to crosses on cross detail page.
 287 ## Cross properties for cassavabase
 288 cross_properties Tag Number,Pollination Date,Number of Bags,Number of Flowers,Number of Fruits,Number of Seeds
 289
 290 ##Cross properties for yambase
 291 ##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
 292
 293 ##Cross properties for musabase
 294 ##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
 295
 296
 297 ## Cross additional info
 298 cross_additional_info female_focus_trait,male_focus_trait,female_source_trial,male_source_trial
 299 cross_additional_info_header Female Focus Trait,Male Focus Trait,Female Source Trial,Male Source Trial
 300
 301 ##
 302 genotyping_facilities None,Cornell IGD,DArT,Intertek,IBRC Japan,BGI
 303 ##
 304 ##
 305 sampling_facilities In-lab,Cornell IGD,DArT,Intertek,IBRC Japan,BGI
 306 ##
 307
 308 ##
 309 management_factor_types Fertilizer,Fungicide,Irrigation,Drought,Herbicide,Weeding,Pruning,Hormone treatment,Light treatment
 310 ##
 311
 312 ##
 313 design_types Completely Randomized,Complete Block,Resolvable Row-Column,Doubly-Resolvable Row-Column,Augmented Row-Column,Alpha Lattice,Lattice,Augmented,Modified Augmented Design,Nursery/Greenhouse,Split Plot,Partially Replicated,Westcott
 314 ##
 315
 316 ##
 317 trial_activities Started Phenotyping, Phenotyping Completed, Data Cleaning Completed, Data Analysis Completed
 318 ##
 319
 320 ### properties for ordering system (required 2 sets of order properties: order_properties and order_properties_dialog)
 321 ### customized dropdown menu can be included in the order_properties_dialog. Dropdown menu can be linked with each property by using ":"
 322 ### for example Facility and Experiment Type properties have customized dropdown menu:
 323 #order_properties Quantity,Facility,Scientist,Required by Date,Experiment Name,Experiment Type
 324 #order_properties_dialog Quantity,Facility:green house:growth chamber,Scientist,Required by Date,Experiment Name,Experiment Type:seed production:experimentation
 325
 326 ###for setting up a single step submission use the following:
 327 #ordering_type single_step
 328 ##two steps (adding to your cart first) is by default
 329
 330 order_properties Quantity,Comments
 331 order_properties_dialog Quantity,Comments
 332
 333 ##
 334
 335 <feature SGN::Feature::FeaturePages>
 336     enabled      1
 337 </feature>
 338 <feature SGN::Feature::LocusPages>
 339     enabled      1
 340 </feature>
 341 #
 342 # default GBrowse2 configuration, for a Debian gbrowse2 installation
 343 <feature SGN::Feature::GBrowse2>
 344     enabled      1
 345     perl_inc     /usr/local/share/website/gbrowse/lib/perl5
 346     tmp_dir      /usr/local/share/website/tmp/gbrowse
 347     cgi_url      /gbrowse/bin
 348     static_url   /gbrowse/static
 349     run_mode     fastcgi
 350     cgi_bin      /usr/lib/cgi-bin/gbrowse
 351     static_dir   /usr/local/share/website/gbrowse/htdocs
 352 </feature>
 353 #
 354 # default ITAG config
 355 <feature SGN::Feature::ITAG>
 356     enabled         1
 357     pipeline_base   /export/shared/tomato_genome/itagpipeline/itag
 358     releases_base   /export/prod/private/genomes/solanum_lycopersicum/annotation
 359 </feature>
 360 #
 361 cview_db_backend    cxgn
 362
 363 #how to find blast stuff
 364 blast_path                ""
 365 blast_db_path             /export/prod/blast/databases/current
 366 preselected_blastdb       224
 367 jbrowse_path              /jbrowse_solgenomics/?data=data/json
 368
 369 # Set the the Blast DB (by species and reference genome) used for getting the marker flanking sequence
 370 # flanking_sequence_blast_db  Triticum aestivum|RefSeq_v1|4,Triticum durum|Triticum durum|5
 371 flanking_sequence_blast_db
 372
 373 #bin directory used by cluster nodes
 374 cluster_shared_bindir /export/prod/bin
 375 #
 376 #the shared temp directory used by cluster nodes
 377 cluster_shared_tempdir    /export/prod/tmp
 378 gbs_temp_data  /export/prod/public
 379
 380 cluster_host ""
 381
 382 #
 383 #how verbose we want the warnings to be in the apache error log
 384 verbose_warnings          1
 385 #
 386 # Insitu file locations
 387 insitu_fullsize_dir       /export/prod/public/images/insitu/processed
 388 insitu_fullsize_url       /export/images/insitu/processed
 389 insitu_display_dir        /export/prod/public/images/insitu/display
 390 insitu_display_url        /export/images/insitu/display
 391 insitu_input_dir          /export/prod/public/images/insitu/incoming
 392 #
 393 #path to our production_ftp site
 394 ftpsite_root              /export/prod/public
 395 ftpsite_url               ftp://ftp.solgenomics.net
 396 #path to the pucebaboon temperature sensor file:
 397 pucebaboon_file        /export/prod/public/digitemp.out
 398 #
 399 #path for archving uploaded files
 400 archive_path     /export/prod/sgn_archive
 401
 402 #path for Cache::File system. used by CXGN::Dataset::Cache
 403 cache_file_path /export/prod/sgn_cache
 404
 405 #site overall identifier prefix used for site specific data
 406 #such as stocks, unignes (yet to be implemented) and other datatypes
 407 #for example, uploading barcode phenotyping data will not work without this key (see L<CXGN::Stock::StockBarcode> )
 408 identifier_prefix   SGN
 409
 410 #default genotyping protocol to use:
 411 default_genotyping_protocol undefined(set this in sgn_local.conf)
 412
 413 genotyping_server_host NULL
 414 genotyping_server_username NULL
 415 genotyping_server_password NULL
 416 genotyping_server_token NULL
 417
 418 #HIDAP Shiny Server Support
 419 hidap_enabled    0
 420
 421 #BrAPI params
 422 supportedCrop    Cassava
 423 brapi_require_login 0
 424
 425 #Expression Atlas Connection
 426 has_expression_atlas    0
 427 expression_atlas_url    0
 428
 429 #Homepage controller customization
 430 homepage_display_phenotype_uploads 0
 431
 432 ## banana ordering system
 433 ordering_service_name NULL
 434 ordering_service_url https://ona.io
 435 ordering_service_username ONAUSER
 436 ordering_service_password ONAPASS
 437
 438 #ODK Services
 439 odk_crossing_data_service_name NULL
 440 odk_crossing_data_service_url https://ona.io
 441 odk_crossing_data_service_username ONAUSER
 442 odk_crossing_data_service_password ONAPASS
 443 odk_crossing_data_test_form_name NULL
 444 odk_crossing_data_separate_wishlist_by_location 0
 445 odk_phenotyping_data_service_name NULL
 446 odk_phenotyping_data_service_url https://bio.smap.com.au
 447 odk_phenotyping_data_service_username SMAPUSER
 448 odk_phenotyping_data_service_password SMAPPASS
 449 crontab_file NULL
 450 crontab_log_filepath NULL
 451
 452 #Authorized Clients for SSO
 453 authorized_clients_JSON {"TEST://":"TEST","fieldbook://":"FieldBook App","https://apps.cipotato.org/hidap_sbase/":"HIDAP","https://fieldbook.phenoapps.org/":"fieldbook","https://climmob.net":"ClimMob"}
 454
 455 simsearch_datadir /home/production/simsearch_data
 456
 457 version sgn-311.0-236
 458 version_updated 2021-12-23T19:04:41Z