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