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 project_name SGN
  33
  34 disable_login 0
  35 default_login_janedoe 0
  36 require_login 0
  37 brapi_require_login 0
  38 brapi_GET any
  39 brapi_POST submitter,curator
  40 brapi_PUT submitter,curator
  41 brapi_OPTIONS any
  42
  43 # Cluster backend
  44 backend Slurm
  45
  46 # the species that should be preselected in a list of species
  47 #
  48 preferred_species
  49
  50 # who is the web server user for chowning and emailing.  need to set
  51 # these manually under Apache mod_perl for example, because the server
  52 # runs under a different user than when it starts.
  53 www_user                 __USERNAME__
  54 www_group                __GROUPNAME__
  55
  56 # when true, server removes its tempfiles when the app is started
  57 clear_tempfiles_on_restart  1
  58
  59 solqtl /export/prod/tmp/solqtl/__USERNAME__
  60 ##### other config variables #####
  61
  62 dbsearchpath   sgn
  63 dbsearchpath   public
  64 dbsearchpath   annotation
  65 dbsearchpath   genomic
  66 dbsearchpath   insitu
  67 dbsearchpath   metadata
  68 dbsearchpath   pheno_population
  69 dbsearchpath   phenome
  70 dbsearchpath   physical
  71 dbsearchpath   tomato_gff
  72 dbsearchpath   biosource
  73 dbsearchpath   gem
  74 dbsearchpath   sgn_people
  75
  76 <DatabaseConnection sgn_test>
  77         #password   set_this_please
  78         dsn   dbi:Pg:host=localhost;dbname=cxgn
  79         user   postgres
  80         search_path   public
  81         search_path   sgn
  82         search_path   annotation
  83         search_path   genomic
  84         search_path   insitu
  85         search_path   metadata
  86         search_path   pheno_population
  87         search_path   phenome
  88         search_path   physical
  89         search_path   tomato_gff
  90         search_path   biosource
  91         search_path   gem
  92         search_path   sgn_people
  93 </DatabaseConnection>
  94
  95 ### Cview configuration parameters
  96 <Controller::Cview>
  97         cview_default_map_id 9
  98 </Controller::Cview>
  99
 100 ##Github access token used for contact form posting of issues
 101 github_access_token NULL
 102
 103 ##NOAA National Climatic Data Center Access token
 104 noaa_ncdc_access_token NULL
 105
 106 ## captcha keys for the production site
 107 #captcha_private_key  6Lc__9YSAAAAANcTczARhRnZRkKmzWjnhipyqI6f
 108 #captcha_public_key   6Lc__9YSAAAAAH2ODL2FlR8jKa2Ms9i9d_0ziBWr
 109
 110 ### backcompat variables for the various static content types
 111 # relative URL and absolute path for static datasets
 112 static_datasets_url       /data
 113 static_datasets_path      /export/prod/public
 114
 115 # relative URL and absoluate path for static site content
 116 static_content_url        /static_content
 117 static_content_path       /export/prod/public/sgn_static_content
 118 homepage_files_dir        /export/prod/public/sgn_static_content/homepage
 119
 120 # this needs to be here rather than in the CGI controller itself to
 121 # work around a bug in all but the most recent
 122 # Catalyst::Controller::CGIBin
 123 <Controller::CGI>
 124     cgi_dir   __path_to(cgi-bin)__
 125 </Controller::CGI>
 126
 127 <Controller::Genomes::Tomato>
 128    bac_publish_subdir tomato_genome/bacs
 129 </Controller::Genomes::Tomato>
 130
 131 <Plugin::SmartURI>
 132                disposition host-header   # application-wide
 133                uri_class   URI::SmartURI # by default
 134 </Plugin::SmartURI>
 135
 136
 137 <View::Email::ErrorEmail>
 138     <default>
 139         content_type  text/plain
 140         to            sgn-bugs@solgenomics.net
 141         from          sgn-bugs@solgenomics.net
 142         charset       utf-8
 143     </default>
 144     dump_skip_class   Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet  DBIx::Class::Row  HTML::Mason::Interp
 145 </View::Email::ErrorEmail>
 146
 147 # should we send emails, if we are a production server? this can be
 148 # used to turn off emails if we are being bombarded.
 149 admin_email              sgn-feedback@solgenomics.net
 150 feedback_email           sgn-feedback@solgenomics.net
 151 bugs_email               sgn-bugs@solgenomics.net
 152 email                    sgn-feedback@solgenomics.net
 153 contact_form_email       contactform@solgenomics.net
 154 cluster_job_email        cluster-jobs@solgenomics.net
 155 tokn_email               scp78@cornell.edu
 156 disable_emails           0
 157
 158 # External SMTP Server to send emails
 159 smtp_server
 160 smtp_layer  ssl
 161 smtp_auth   AUTO
 162 smtp_port
 163 smtp_login
 164 smtp_pass
 165 smtp_from
 166
 167 # URL of the canonical, main production site
 168 main_production_site_url  http://solgenomics.net
 169
 170 #is there a system message text file somewhere we should be displaying?
 171 system_message_file       __HOME__/system_message.txt
 172 # defaults to /tmp/<user>/SGN-site
 173 #tempfiles_base
 174
 175
 176 tempfiles_base            ""
 177 #
 178
 179 # where to run cluster jobs - nothing means "batch" queue
 180 #web_cluster_queue
 181
 182
 183 # where to run cluster jobs
 184 web_cluster_queue        batch
 185
 186
 187 #is this a mirror of SGN, or the real thing?
 188 is_mirror                 0
 189 #
 190 # how to find cosii_files for markerinfo.pl
 191 cosii_files               /export/cosii2
 192 #
 193 # log files, ABSOLUTE PATHS
 194 error_log                 /var/log/sgn-site/error.log
 195 access_log                /var/log/sgn-site/access.log
 196 rewrite_log               /var/log/sgn-site/rewrite.log
 197 blast_log                 /export/prod/tmp/blast/blast.log
 198 #
 199 # paths to stuff
 200 hmmsearch_location        hmmsearch
 201 intron_finder_database    /export/prod/public/intron_finder_database
 202 #
 203 trace_path                /export/prod/public/chromatograms
 204 image_dir                 /images/image_files
 205 image_path                /export/prod/public/images
 206 tempfiles_subdir          /static/documents/tempfiles
 207 submit_dir                /data/shared/submit-uploads
 208 programs_subdir           /programs
 209 documents_subdir          /documents
 210 conf_subdir               /conf
 211 support_data_subdir       /support_data
 212 #
 213 #stock tempfiles (for downloading phenotype and genotype raw data)
 214 stock_tempfiles           /static/documents/tempfiles/stock
 215 #weblogo tempfiles for motifs finder tools
 216 tmp_weblogo_path          /static/documents/tempfiles/
 217 #
 218 #currently our cookies encrypt stuff, so this is just a random string to use to do that
 219 cookie_encryption_key     bo9yie2JeeVee6ouAhch9aomeesieJ3iShae8aa8
 220 #
 221 # where the genefamily info is stored
 222 genefamily_dir            /export/prod/private/genomes/genefamily/
 223 #
 224
 225 ##
 226 # 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
 227 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
 228
 229 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
 230 ##
 231
 232 ## Cross properties that should be displayed and allowed to be added to crosses on cross detail page.
 233 ## Cross properties for cassavabase
 234 cross_properties Tag Number,Pollination Date,Number of Bags,Number of Flowers,Number of Fruits,Number of Seeds
 235
 236 ##Cross properties for yambase
 237 ##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
 238
 239 ##Cross properties for musabase
 240 ##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
 241
 242 ## Cross additional info
 243 cross_additional_info female_focus_trait,male_focus_trait,female_source_trial,male_source_trial
 244 cross_additional_info_header Female Focus Trait,Male Focus Trait,Female Source Trial,Male Source Trial
 245
 246 ##
 247 genotyping_facilities None,Cornell IGD,DArT,Intertek,IBRC Japan,BGI
 248 ##
 249 ##
 250 sampling_facilities In-lab,Cornell IGD,DArT,Intertek,IBRC Japan,BGI
 251 ##
 252
 253 ##
 254 management_factor_types Fertilizer,Fungicide,Irrigation,Drought,Herbicide,Weeding,Pruning,Hormone treatment,Light treatment
 255 ##
 256
 257 ##
 258 design_types Completely Randomized,Complete Block,Alpha Lattice,Lattice,Augmented,Modified Augmented Design,Nursery/Greenhouse,Split Plot,Partially Replicated,Westcott
 259 ##
 260
 261 <feature SGN::Feature::FeaturePages>
 262     enabled      1
 263 </feature>
 264 <feature SGN::Feature::LocusPages>
 265     enabled      1
 266 </feature>
 267 #
 268 # default GBrowse2 configuration, for a Debian gbrowse2 installation
 269 <feature SGN::Feature::GBrowse2>
 270     enabled      1
 271     perl_inc     /usr/local/share/website/gbrowse/lib/perl5
 272     tmp_dir      /usr/local/share/website/tmp/gbrowse
 273     cgi_url      /gbrowse/bin
 274     static_url   /gbrowse/static
 275     run_mode     fastcgi
 276     cgi_bin      /usr/lib/cgi-bin/gbrowse
 277     static_dir   /usr/local/share/website/gbrowse/htdocs
 278 </feature>
 279 #
 280 # default ITAG config
 281 <feature SGN::Feature::ITAG>
 282     enabled         1
 283     pipeline_base   /export/shared/tomato_genome/itagpipeline/itag
 284     releases_base   /export/prod/private/genomes/solanum_lycopersicum/annotation
 285 </feature>
 286 #
 287 cview_db_backend    cxgn
 288
 289 #how to find blast stuff
 290 blast_path                ""
 291 blast_db_path             /export/prod/blast/databases/current
 292 preselected_blastdb       224
 293 jbrowse_path              /jbrowse_solgenomics/?data=data/json
 294
 295 #bin directory used by cluster nodes
 296 cluster_shared_bindir /export/prod/bin
 297 #
 298 #the shared temp directory used by cluster nodes
 299 cluster_shared_tempdir    /export/prod/tmp
 300 gbs_temp_data  /export/prod/public
 301
 302 cluster_host ""
 303
 304 #
 305 #how verbose we want the warnings to be in the apache error log
 306 verbose_warnings          1
 307 #
 308 # Insitu file locations
 309 insitu_fullsize_dir       /export/prod/public/images/insitu/processed
 310 insitu_fullsize_url       /export/images/insitu/processed
 311 insitu_display_dir        /export/prod/public/images/insitu/display
 312 insitu_display_url        /export/images/insitu/display
 313 insitu_input_dir          /export/prod/public/images/insitu/incoming
 314 #
 315 #path to our production_ftp site
 316 ftpsite_root              /export/prod/public
 317 ftpsite_url               ftp://ftp.solgenomics.net
 318 #path to the pucebaboon temperature sensor file:
 319 pucebaboon_file        /export/prod/public/digitemp.out
 320 #
 321 #path for archving uploaded files
 322 archive_path     /export/prod/sgn_archive
 323
 324 #path for Cache::File system. used by CXGN::Dataset::Cache
 325 cache_file_path /export/prod/sgn_cache
 326
 327 #site overall identifier prefix used for site specific data
 328 #such as stocks, unignes (yet to be implemented) and other datatypes
 329 #for example, uploading barcode phenotyping data will not work without this key (see L<CXGN::Stock::StockBarcode> )
 330 identifier_prefix   SGN
 331
 332 #default genotyping protocol to use:
 333 default_genotyping_protocol undefined(set this in sgn_local.conf)
 334
 335 genotyping_server_host NULL
 336 genotyping_server_username NULL
 337 genotyping_server_password NULL
 338 genotyping_server_token NULL
 339
 340 #HIDAP Shiny Server Support
 341 hidap_enabled    0
 342
 343 #BrAPI params
 344 supportedCrop    Cassava
 345 brapi_require_login 0
 346
 347 #Expression Atlas Connection
 348 has_expression_atlas    0
 349 expression_atlas_url    0
 350
 351 #Homepage controller customization
 352 homepage_display_phenotype_uploads 0
 353
 354 #ODK Services
 355 odk_crossing_data_service_name NULL
 356 odk_crossing_data_service_url https://ona.io
 357 odk_crossing_data_service_username ONAUSER
 358 odk_crossing_data_service_password ONAPASS
 359 odk_crossing_data_test_form_name NULL
 360 odk_crossing_data_separate_wishlist_by_location 0
 361 odk_phenotyping_data_service_name NULL
 362 odk_phenotyping_data_service_url https://bio.smap.com.au
 363 odk_phenotyping_data_service_username SMAPUSER
 364 odk_phenotyping_data_service_password SMAPPASS
 365 crontab_file NULL
 366 crontab_log_filepath NULL
 367
 368 #Authorized Clients for SSO
 369 authorized_clients_JSON {"TEST://":"TEST","fieldbook://":"FieldBook App","https://apps.cipotato.org/hidap_sbase/":"HIDAP"}