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