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