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