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