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   db.sgn.cornell.edu
   9 dbname   cxgn-test
  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_cv_name cassava_trait
  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 # For Trait Search page
  32 trait_variable_onto_root_namespaces CO_322 (Cassava Ontology), UO (Units), CASSTISS (Cass tissues), COMP (Composed Variables)
  33
  34 project_name SGN
  35
  36 disable_login 0
  37 default_login_janedoe 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 ## captcha keys for the production site
 100 #captcha_private_key  6Lc__9YSAAAAANcTczARhRnZRkKmzWjnhipyqI6f
 101 #captcha_public_key   6Lc__9YSAAAAAH2ODL2FlR8jKa2Ms9i9d_0ziBWr
 102
 103 ### backcompat variables for the various static content types
 104 # relative URL and absolute path for static datasets
 105 static_datasets_url       /data
 106 static_datasets_path      /export/prod/public
 107
 108 # relative URL and absoluate path for static site content
 109 static_content_url        /static_content
 110 static_content_path       /export/prod/public/sgn_static_content
 111 homepage_files_dir        /export/prod/public/sgn_static_content/homepage
 112
 113 # this needs to be here rather than in the CGI controller itself to
 114 # work around a bug in all but the most recent
 115 # Catalyst::Controller::CGIBin
 116 <Controller::CGI>
 117     cgi_dir   __path_to(cgi-bin)__
 118 </Controller::CGI>
 119
 120 <Controller::Genomes::Tomato>
 121    bac_publish_subdir tomato_genome/bacs
 122 </Controller::Genomes::Tomato>
 123
 124 <Plugin::SmartURI>
 125                disposition host-header   # application-wide
 126                uri_class   URI::SmartURI # by default
 127 </Plugin::SmartURI>
 128
 129
 130 <View::Email::ErrorEmail>
 131     <default>
 132         content_type  text/plain
 133         to            sgn-bugs@solgenomics.net
 134         from          sgn-bugs@solgenomics.net
 135         charset       utf-8
 136     </default>
 137     dump_skip_class   Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet  DBIx::Class::Row  HTML::Mason::Interp
 138 </View::Email::ErrorEmail>
 139
 140 # should we send emails, if we are a production server? this can be
 141 # used to turn off emails if we are being bombarded.
 142 admin_email              sgn-feedback@solgenomics.net
 143 feedback_email           sgn-feedback@solgenomics.net
 144 bugs_email               sgn-bugs@solgenomics.net
 145 email                    sgn-feedback@solgenomics.net
 146 contact_form_email       contactform@solgenomics.net
 147 tokn_email               scp78@cornell.edu
 148 disable_emails           0
 149
 150 # External SMTP Server to send emails
 151 smtp_server
 152 smtp_port
 153 smtp_user
 154 smtp_pass
 155 smtp_from
 156
 157 # URL of the canonical, main production site
 158 main_production_site_url  http://solgenomics.net
 159
 160 #is there a system message text file somewhere we should be displaying?
 161 system_message_file       __HOME__/system_message.txt
 162 # defaults to /tmp/<user>/SGN-site
 163 #tempfiles_base
 164
 165
 166 tempfiles_base            ""
 167 #
 168
 169 # where to run cluster jobs - nothing means "batch" queue
 170 #web_cluster_queue
 171
 172
 173 # where to run cluster jobs
 174 web_cluster_queue        batch
 175
 176
 177 #is this a mirror of SGN, or the real thing?
 178 is_mirror                 0
 179 #
 180 # how to find cosii_files for markerinfo.pl
 181 cosii_files               /export/cosii2
 182 #
 183 # log files, ABSOLUTE PATHS
 184 error_log                 /var/log/sgn-site/error.log
 185 access_log                /var/log/sgn-site/access.log
 186 rewrite_log               /var/log/sgn-site/rewrite.log
 187 blast_log                 /export/prod/tmp/blast/blast.log
 188 #
 189 # paths to stuff
 190 hmmsearch_location        hmmsearch
 191 intron_finder_database    /export/prod/public/intron_finder_database
 192 #
 193 trace_path                /export/prod/public/chromatograms
 194 image_dir                 /images/image_files
 195 image_path                /export/prod/public/images
 196 tempfiles_subdir          /static/documents/tempfiles
 197 submit_dir                /data/shared/submit-uploads
 198 programs_subdir           /programs
 199 documents_subdir          /documents
 200 conf_subdir               /conf
 201 support_data_subdir       /support_data
 202 #
 203 #stock tempfiles (for downloading phenotype and genotype raw data)
 204 stock_tempfiles           /static/documents/tempfiles/stock
 205 #
 206 #currently our cookies encrypt stuff, so this is just a random string to use to do that
 207 cookie_encryption_key     bo9yie2JeeVee6ouAhch9aomeesieJ3iShae8aa8
 208 #
 209 # where the genefamily info is stored
 210 genefamily_dir            /export/prod/private/genomes/genefamily/
 211 #
 212
 213 ##
 214 # stock properties that should be displayed and allowed to be edited in the "additional information" section
 215 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
 216 ##
 217
 218 ## Cross properties that should be displayed and allowed to be added to crosses on cross detail page.
 219 ## Cross properties for cassavabase
 220 cross_properties Tag Number,Pollination Date,Number of Bags,Number of Flowers,Number of Fruits,Number of Seeds
 221
 222 ##Cross properties for yambase
 223 ##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
 224
 225 ##Cross properties for musabase
 226 ##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
 227
 228 <feature SGN::Feature::FeaturePages>
 229     enabled      1
 230 </feature>
 231 <feature SGN::Feature::LocusPages>
 232     enabled      1
 233 </feature>
 234 #
 235 # default GBrowse2 configuration, for a Debian gbrowse2 installation
 236 <feature SGN::Feature::GBrowse2>
 237     enabled      1
 238     perl_inc     /usr/local/share/website/gbrowse/lib/perl5
 239     tmp_dir      /usr/local/share/website/tmp/gbrowse
 240     cgi_url      /gbrowse/bin
 241     static_url   /gbrowse/static
 242     run_mode     fastcgi
 243     cgi_bin      /usr/lib/cgi-bin/gbrowse
 244     static_dir   /usr/local/share/website/gbrowse/htdocs
 245 </feature>
 246 #
 247 # default ITAG config
 248 <feature SGN::Feature::ITAG>
 249     enabled         1
 250     pipeline_base   /export/shared/tomato_genome/itagpipeline/itag
 251     releases_base   /export/prod/private/genomes/solanum_lycopersicum/annotation
 252 </feature>
 253 #
 254 cview_db_backend    cxgn
 255
 256 #how to find blast stuff
 257 blast_path                ""
 258 blast_db_path             /export/prod/blast/databases/current
 259 preselected_blastdb       224
 260 jbrowse_path              /jbrowse_solgenomics/?data=data/json
 261
 262
 263 #bin directory used by cluster nodes
 264 cluster_shared_bindir /export/prod/bin
 265 #
 266 #the shared temp directory used by cluster nodes
 267 cluster_shared_tempdir    /export/prod/tmp
 268 gbs_temp_data  /export/prod/public
 269
 270 #
 271 #how verbose we want the warnings to be in the apache error log
 272 verbose_warnings          1
 273 #
 274 # Insitu file locations
 275 insitu_fullsize_dir       /export/prod/public/images/insitu/processed
 276 insitu_fullsize_url       /export/images/insitu/processed
 277 insitu_display_dir        /export/prod/public/images/insitu/display
 278 insitu_display_url        /export/images/insitu/display
 279 insitu_input_dir          /export/prod/public/images/insitu/incoming
 280 #
 281 #path to our production_ftp site
 282 ftpsite_root              /export/prod/public
 283 ftpsite_url               ftp://ftp.solgenomics.net
 284 #path to the pucebaboon temperature sensor file:
 285 pucebaboon_file        /export/prod/public/digitemp.out
 286 #
 287 #path for archving uploaded files
 288 archive_path     /export/prod/sgn_archive
 289
 290 #site overall identifier prefix used for site specific data
 291 #such as stocks, unignes (yet to be implemented) and other datatypes
 292 #for example, uploading barcode phenotyping data will not work without this key (see L<CXGN::Stock::StockBarcode> )
 293 identifier_prefix   SGN
 294
 295 #default genotyping protocol to use:
 296 default_genotyping_protocol undefined(set this in sgn_local.conf)
 297
 298 genotyping_server_host NULL
 299 genotyping_server_username NULL
 300 genotyping_server_password NULL
 301 genotyping_server_token NULL
 302
 303 #HIDAP Shiny Server Support
 304 hidap_enabled    0
 305
 306 #BrAPI params
 307 supportedCrop    Cassava
 308 brapi_require_login 0
 309
 310 #Expression Atlas Connection
 311 has_expression_atlas    0
 312 expression_atlas_url    0
 313
 314 #Homepage controller customization
 315 homepage_display_phenotype_uploads 0
 316
 317 #ODK Services
 318 odk_crossing_data_service_name NULL
 319 odk_crossing_data_service_url https://ona.io
 320 odk_crossing_data_service_username ONAUSER
 321 odk_crossing_data_service_password ONAPASS
 322 odk_crossing_data_test_form_name NULL
 323 odk_crossing_data_separate_wishlist_by_location 0
 324 odk_phenotyping_data_service_name NULL
 325 odk_phenotyping_data_service_url https://bio.smap.com.au
 326 odk_phenotyping_data_service_username SMAPUSER
 327 odk_phenotyping_data_service_password SMAPPASS
 328 crontab_file NULL
 329 crontab_log_filepath NULL