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
  18 composable_cvs trait,object,tod,toy,unit,method
  19 composable_cvs_allowed_combinations Agronomic|trait+toy,Metabolic|trait+object+tod+toy+unit+method
  20 composable_cvterm_delimiter |
  21 composable_cvterm_format concise
  22 composable_tod_root_cvterm "time of day|TIME:0000001"
  23 composable_toy_root_cvterm "time of year|TIME:0000005"
  24 composable_gen_root_cvterm "generation|TIME:0000072"
  25 composable_evt_root_cvterm "event|TIME:0000477"
  26 allow_observation_variable_submission_interface 0
  27 trait_ontology_db_name SP
  28 # For displaying ontologies in Ontology Browser
  29 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)
  30
  31 project_name SGN
  32
  33 disable_login 0
  34 default_login_janedoe 0
  35 require_login 0
  36
  37 # Cluster backend
  38 backend Slurm
  39
  40 # the species that should be preselected in a list of species
  41 #
  42 preferred_species
  43
  44 # who is the web server user for chowning and emailing.  need to set
  45 # these manually under Apache mod_perl for example, because the server
  46 # runs under a different user than when it starts.
  47 www_user                 __USERNAME__
  48 www_group                __GROUPNAME__
  49
  50 # when true, server removes its tempfiles when the app is started
  51 clear_tempfiles_on_restart  1
  52
  53 solqtl /export/prod/tmp/solqtl/__USERNAME__
  54 ##### other config variables #####
  55
  56 dbsearchpath   sgn
  57 dbsearchpath   public
  58 dbsearchpath   annotation
  59 dbsearchpath   genomic
  60 dbsearchpath   insitu
  61 dbsearchpath   metadata
  62 dbsearchpath   pheno_population
  63 dbsearchpath   phenome
  64 dbsearchpath   physical
  65 dbsearchpath   tomato_gff
  66 dbsearchpath   biosource
  67 dbsearchpath   gem
  68 dbsearchpath   sgn_people
  69
  70 <DatabaseConnection sgn_test>
  71         #password   set_this_please
  72         dsn   dbi:Pg:host=localhost;dbname=cxgn
  73         user   postgres
  74         search_path   public
  75         search_path   sgn
  76         search_path   annotation
  77         search_path   genomic
  78         search_path   insitu
  79         search_path   metadata
  80         search_path   pheno_population
  81         search_path   phenome
  82         search_path   physical
  83         search_path   tomato_gff
  84         search_path   biosource
  85         search_path   gem
  86         search_path   sgn_people
  87 </DatabaseConnection>
  88
  89 ### Cview configuration parameters
  90 <Controller::Cview>
  91         cview_default_map_id 9
  92 </Controller::Cview>
  93
  94 ##Github access token used for contact form posting of issues
  95 github_access_token NULL
  96
  97 ##NOAA National Climatic Data Center Access token
  98 noaa_ncdc_access_token NULL
  99
 100 ## captcha keys for the production site
 101 #captcha_private_key  6Lc__9YSAAAAANcTczARhRnZRkKmzWjnhipyqI6f
 102 #captcha_public_key   6Lc__9YSAAAAAH2ODL2FlR8jKa2Ms9i9d_0ziBWr
 103
 104 ### backcompat variables for the various static content types
 105 # relative URL and absolute path for static datasets
 106 static_datasets_url       /data
 107 static_datasets_path      /export/prod/public
 108
 109 # relative URL and absoluate path for static site content
 110 static_content_url        /static_content
 111 static_content_path       /export/prod/public/sgn_static_content
 112 homepage_files_dir        /export/prod/public/sgn_static_content/homepage
 113
 114 # this needs to be here rather than in the CGI controller itself to
 115 # work around a bug in all but the most recent
 116 # Catalyst::Controller::CGIBin
 117 <Controller::CGI>
 118     cgi_dir   __path_to(cgi-bin)__
 119 </Controller::CGI>
 120
 121 <Controller::Genomes::Tomato>
 122    bac_publish_subdir tomato_genome/bacs
 123 </Controller::Genomes::Tomato>
 124
 125 <Plugin::SmartURI>
 126                disposition host-header   # application-wide
 127                uri_class   URI::SmartURI # by default
 128 </Plugin::SmartURI>
 129
 130
 131 <View::Email::ErrorEmail>
 132     <default>
 133         content_type  text/plain
 134         to            sgn-bugs@solgenomics.net
 135         from          sgn-bugs@solgenomics.net
 136         charset       utf-8
 137     </default>
 138     dump_skip_class   Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet  DBIx::Class::Row  HTML::Mason::Interp
 139 </View::Email::ErrorEmail>
 140
 141 # should we send emails, if we are a production server? this can be
 142 # used to turn off emails if we are being bombarded.
 143 admin_email              sgn-feedback@solgenomics.net
 144 feedback_email           sgn-feedback@solgenomics.net
 145 bugs_email               sgn-bugs@solgenomics.net
 146 email                    sgn-feedback@solgenomics.net
 147 contact_form_email       contactform@solgenomics.net
 148 tokn_email               scp78@cornell.edu
 149 disable_emails           0
 150
 151 # External SMTP Server to send emails
 152 smtp_server
 153 smtp_layer  ssl
 154 smtp_auth   AUTO
 155 smtp_port
 156 smtp_login
 157 smtp_pass
 158 smtp_from
 159
 160 # URL of the canonical, main production site
 161 main_production_site_url  http://solgenomics.net
 162
 163 #is there a system message text file somewhere we should be displaying?
 164 system_message_file       __HOME__/system_message.txt
 165 # defaults to /tmp/<user>/SGN-site
 166 #tempfiles_base
 167
 168
 169 tempfiles_base            ""
 170 #
 171
 172 # where to run cluster jobs - nothing means "batch" queue
 173 #web_cluster_queue
 174
 175
 176 # where to run cluster jobs
 177 web_cluster_queue        batch
 178
 179
 180 #is this a mirror of SGN, or the real thing?
 181 is_mirror                 0
 182 #
 183 # how to find cosii_files for markerinfo.pl
 184 cosii_files               /export/cosii2
 185 #
 186 # log files, ABSOLUTE PATHS
 187 error_log                 /var/log/sgn-site/error.log
 188 access_log                /var/log/sgn-site/access.log
 189 rewrite_log               /var/log/sgn-site/rewrite.log
 190 blast_log                 /export/prod/tmp/blast/blast.log
 191 #
 192 # paths to stuff
 193 hmmsearch_location        hmmsearch
 194 intron_finder_database    /export/prod/public/intron_finder_database
 195 #
 196 trace_path                /export/prod/public/chromatograms
 197 image_dir                 /images/image_files
 198 image_path                /export/prod/public/images
 199 tempfiles_subdir          /static/documents/tempfiles
 200 submit_dir                /data/shared/submit-uploads
 201 programs_subdir           /programs
 202 documents_subdir          /documents
 203 conf_subdir               /conf
 204 support_data_subdir       /support_data
 205 #
 206 #stock tempfiles (for downloading phenotype and genotype raw data)
 207 stock_tempfiles           /static/documents/tempfiles/stock
 208 #
 209 #currently our cookies encrypt stuff, so this is just a random string to use to do that
 210 cookie_encryption_key     bo9yie2JeeVee6ouAhch9aomeesieJ3iShae8aa8
 211 #
 212 # where the genefamily info is stored
 213 genefamily_dir            /export/prod/private/genomes/genefamily/
 214 #
 215
 216 ##
 217 # stock properties that should be displayed and allowed to be edited in the "additional information" section
 218 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
 219 ##
 220
 221 ## Cross properties that should be displayed and allowed to be added to crosses on cross detail page.
 222 ## Cross properties for cassavabase
 223 cross_properties Tag Number,Pollination Date,Number of Bags,Number of Flowers,Number of Fruits,Number of Seeds
 224
 225 ##Cross properties for yambase
 226 ##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
 227
 228 ##Cross properties for musabase
 229 ##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
 230
 231 <feature SGN::Feature::FeaturePages>
 232     enabled      1
 233 </feature>
 234 <feature SGN::Feature::LocusPages>
 235     enabled      1
 236 </feature>
 237 #
 238 # default GBrowse2 configuration, for a Debian gbrowse2 installation
 239 <feature SGN::Feature::GBrowse2>
 240     enabled      1
 241     perl_inc     /usr/local/share/website/gbrowse/lib/perl5
 242     tmp_dir      /usr/local/share/website/tmp/gbrowse
 243     cgi_url      /gbrowse/bin
 244     static_url   /gbrowse/static
 245     run_mode     fastcgi
 246     cgi_bin      /usr/lib/cgi-bin/gbrowse
 247     static_dir   /usr/local/share/website/gbrowse/htdocs
 248 </feature>
 249 #
 250 # default ITAG config
 251 <feature SGN::Feature::ITAG>
 252     enabled         1
 253     pipeline_base   /export/shared/tomato_genome/itagpipeline/itag
 254     releases_base   /export/prod/private/genomes/solanum_lycopersicum/annotation
 255 </feature>
 256 #
 257 cview_db_backend    cxgn
 258
 259 #how to find blast stuff
 260 blast_path                ""
 261 blast_db_path             /export/prod/blast/databases/current
 262 preselected_blastdb       224
 263 jbrowse_path              /jbrowse_solgenomics/?data=data/json
 264
 265
 266 #bin directory used by cluster nodes
 267 cluster_shared_bindir /export/prod/bin
 268 #
 269 #the shared temp directory used by cluster nodes
 270 cluster_shared_tempdir    /export/prod/tmp
 271 gbs_temp_data  /export/prod/public
 272
 273 cluster_host ""
 274
 275 #Directory used for Keras CNN Model Tuning
 276 temp_keras_cnn_model_dir /temp_keras
 277
 278 #
 279 #how verbose we want the warnings to be in the apache error log
 280 verbose_warnings          1
 281 #
 282 # Insitu file locations
 283 insitu_fullsize_dir       /export/prod/public/images/insitu/processed
 284 insitu_fullsize_url       /export/images/insitu/processed
 285 insitu_display_dir        /export/prod/public/images/insitu/display
 286 insitu_display_url        /export/images/insitu/display
 287 insitu_input_dir          /export/prod/public/images/insitu/incoming
 288 #
 289 #path to our production_ftp site
 290 ftpsite_root              /export/prod/public
 291 ftpsite_url               ftp://ftp.solgenomics.net
 292 #path to the pucebaboon temperature sensor file:
 293 pucebaboon_file        /export/prod/public/digitemp.out
 294 #
 295 #path for archving uploaded files
 296 archive_path     /export/prod/sgn_archive
 297
 298 #path for Cache::File system. used by CXGN::Dataset::Cache
 299 cache_file_path /export/prod/sgn_cache
 300
 301 #site overall identifier prefix used for site specific data
 302 #such as stocks, unignes (yet to be implemented) and other datatypes
 303 #for example, uploading barcode phenotyping data will not work without this key (see L<CXGN::Stock::StockBarcode> )
 304 identifier_prefix   SGN
 305
 306 #default genotyping protocol to use:
 307 default_genotyping_protocol undefined(set this in sgn_local.conf)
 308
 309 genotyping_server_host NULL
 310 genotyping_server_username NULL
 311 genotyping_server_password NULL
 312 genotyping_server_token NULL
 313
 314 #HIDAP Shiny Server Support
 315 hidap_enabled    0
 316
 317 #BrAPI params
 318 supportedCrop    Cassava
 319 brapi_require_login 0
 320
 321 #Expression Atlas Connection
 322 has_expression_atlas    0
 323 expression_atlas_url    0
 324
 325 #Homepage controller customization
 326 homepage_display_phenotype_uploads 0
 327
 328 #ODK Services
 329 odk_crossing_data_service_name NULL
 330 odk_crossing_data_service_url https://ona.io
 331 odk_crossing_data_service_username ONAUSER
 332 odk_crossing_data_service_password ONAPASS
 333 odk_crossing_data_test_form_name NULL
 334 odk_crossing_data_separate_wishlist_by_location 0
 335 odk_phenotyping_data_service_name NULL
 336 odk_phenotyping_data_service_url https://bio.smap.com.au
 337 odk_phenotyping_data_service_username SMAPUSER
 338 odk_phenotyping_data_service_password SMAPPASS
 339 crontab_file NULL
 340 crontab_log_filepath NULL