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