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