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 allow_observation_variable_submission_interface 0
  26 trait_cv_name cassava_trait
  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 # For Trait Search page
  31 trait_variable_onto_root_namespaces CO_322 (Cassava Ontology), UO (Units), CASSTISS (Cass tissues), COMP (Composed Variables)
  32
  33 project_name SGN
  34
  35 disable_login 0
  36 default_login_janedoe 0
  37
  38 # Cluster backend
  39 backend Slurm
  40
  41 # the species that should be preselected in a list of species
  42 #
  43 preferred_species
  44
  45 # who is the web server user for chowning and emailing.  need to set
  46 # these manually under Apache mod_perl for example, because the server
  47 # runs under a different user than when it starts.
  48 www_user                 __USERNAME__
  49 www_group                __GROUPNAME__
  50
  51 # when true, server removes its tempfiles when the app is started
  52 clear_tempfiles_on_restart  1
  53
  54 solqtl /export/prod/tmp/solqtl/__USERNAME__
  55 ##### other config variables #####
  56
  57 dbsearchpath   sgn
  58 dbsearchpath   public
  59 dbsearchpath   annotation
  60 dbsearchpath   genomic
  61 dbsearchpath   insitu
  62 dbsearchpath   metadata
  63 dbsearchpath   pheno_population
  64 dbsearchpath   phenome
  65 dbsearchpath   physical
  66 dbsearchpath   tomato_gff
  67 dbsearchpath   biosource
  68 dbsearchpath   gem
  69 dbsearchpath   sgn_people
  70
  71 <DatabaseConnection sgn_test>
  72         #password   set_this_please
  73         dsn   dbi:Pg:host=localhost;dbname=cxgn
  74         user   postgres
  75         search_path   public
  76         search_path   sgn
  77         search_path   annotation
  78         search_path   genomic
  79         search_path   insitu
  80         search_path   metadata
  81         search_path   pheno_population
  82         search_path   phenome
  83         search_path   physical
  84         search_path   tomato_gff
  85         search_path   biosource
  86         search_path   gem
  87         search_path   sgn_people
  88 </DatabaseConnection>
  89
  90 ### Cview configuration parameters
  91 <Controller::Cview>
  92         cview_default_map_id 9
  93 </Controller::Cview>
  94
  95 ##Github access token used for contact form posting of issues
  96 github_access_token NULL
  97
  98 ## captcha keys for the production site
  99 #captcha_private_key  6Lc__9YSAAAAANcTczARhRnZRkKmzWjnhipyqI6f
 100 #captcha_public_key   6Lc__9YSAAAAAH2ODL2FlR8jKa2Ms9i9d_0ziBWr
 101
 102 ### backcompat variables for the various static content types
 103 # relative URL and absolute path for static datasets
 104 static_datasets_url       /data
 105 static_datasets_path      /export/prod/public
 106
 107 # relative URL and absoluate path for static site content
 108 static_content_url        /static_content
 109 static_content_path       /export/prod/public/sgn_static_content
 110 homepage_files_dir        /export/prod/public/sgn_static_content/homepage
 111
 112 # this needs to be here rather than in the CGI controller itself to
 113 # work around a bug in all but the most recent
 114 # Catalyst::Controller::CGIBin
 115 <Controller::CGI>
 116     cgi_dir   __path_to(cgi-bin)__
 117 </Controller::CGI>
 118
 119 <Controller::Genomes::Tomato>
 120    bac_publish_subdir tomato_genome/bacs
 121 </Controller::Genomes::Tomato>
 122
 123 <Plugin::SmartURI>
 124                disposition host-header   # application-wide
 125                uri_class   URI::SmartURI # by default
 126 </Plugin::SmartURI>
 127
 128
 129 <View::Email::ErrorEmail>
 130     <default>
 131         content_type  text/plain
 132         to            sgn-bugs@solgenomics.net
 133         from          sgn-bugs@solgenomics.net
 134         charset       utf-8
 135     </default>
 136     dump_skip_class   Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet  DBIx::Class::Row  HTML::Mason::Interp
 137 </View::Email::ErrorEmail>
 138
 139 # should we send emails, if we are a production server? this can be
 140 # used to turn off emails if we are being bombarded.
 141 admin_email              sgn-feedback@solgenomics.net
 142 feedback_email           sgn-feedback@solgenomics.net
 143 bugs_email               sgn-bugs@solgenomics.net
 144 email                    sgn-feedback@solgenomics.net
 145 contact_form_email       contactform@solgenomics.net
 146 tokn_email               scp78@cornell.edu
 147 disable_emails           0
 148
 149 # URL of the canonical, main production site
 150 main_production_site_url  http://solgenomics.net
 151
 152 #is there a system message text file somewhere we should be displaying?
 153 system_message_file       __HOME__/system_message.txt
 154 # defaults to /tmp/<user>/SGN-site
 155 #tempfiles_base
 156
 157
 158 tempfiles_base            ""
 159 #
 160
 161 # where to run cluster jobs - nothing means "batch" queue
 162 #web_cluster_queue
 163
 164
 165 # where to run cluster jobs
 166 web_cluster_queue        batch
 167
 168
 169 #is this a mirror of SGN, or the real thing?
 170 is_mirror                 0
 171 #
 172 # how to find cosii_files for markerinfo.pl
 173 cosii_files               /export/cosii2
 174 #
 175 # log files, ABSOLUTE PATHS
 176 error_log                 /var/log/sgn-site/error.log
 177 access_log                /var/log/sgn-site/access.log
 178 rewrite_log               /var/log/sgn-site/rewrite.log
 179 blast_log                 /export/prod/tmp/blast/blast.log
 180 #
 181 # paths to stuff
 182 hmmsearch_location        hmmsearch
 183 intron_finder_database    /export/prod/public/intron_finder_database
 184 #
 185 trace_path                /export/prod/public/chromatograms
 186 image_dir                 /images/image_files
 187 image_path                /export/prod/public/images
 188 tempfiles_subdir          /static/documents/tempfiles
 189 submit_dir                /data/shared/submit-uploads
 190 programs_subdir           /programs
 191 documents_subdir          /documents
 192 conf_subdir               /conf
 193 support_data_subdir       /support_data
 194 #
 195 #stock tempfiles (for downloading phenotype and genotype raw data)
 196 stock_tempfiles           /static/documents/tempfiles/stock
 197 #
 198 #currently our cookies encrypt stuff, so this is just a random string to use to do that
 199 cookie_encryption_key     bo9yie2JeeVee6ouAhch9aomeesieJ3iShae8aa8
 200 #
 201 # where the genefamily info is stored
 202 genefamily_dir            /export/prod/private/genomes/genefamily/
 203 #
 204
 205 ##
 206 # stock properties that should be displayed and allowed to be edited in the "additional information" section
 207 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
 208 ##
 209
 210 ## Cross properties that should be displayed and allowed to be added to crosses on cross detail page.
 211 ## Cross properties for cassavabase
 212 cross_properties Tag Number,Pollination Date,Number of Bags,Number of Flowers,Number of Fruits,Number of Seeds
 213
 214 ##Cross properties for yambase
 215 ##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
 216
 217 ##Cross properties for musabase
 218 ##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
 219
 220 <feature SGN::Feature::FeaturePages>
 221     enabled      1
 222 </feature>
 223 <feature SGN::Feature::LocusPages>
 224     enabled      1
 225 </feature>
 226 #
 227 # default GBrowse2 configuration, for a Debian gbrowse2 installation
 228 <feature SGN::Feature::GBrowse2>
 229     enabled      1
 230     perl_inc     /usr/local/share/website/gbrowse/lib/perl5
 231     tmp_dir      /usr/local/share/website/tmp/gbrowse
 232     cgi_url      /gbrowse/bin
 233     static_url   /gbrowse/static
 234     run_mode     fastcgi
 235     cgi_bin      /usr/lib/cgi-bin/gbrowse
 236     static_dir   /usr/local/share/website/gbrowse/htdocs
 237 </feature>
 238 #
 239 # default ITAG config
 240 <feature SGN::Feature::ITAG>
 241     enabled         1
 242     pipeline_base   /export/shared/tomato_genome/itagpipeline/itag
 243     releases_base   /export/prod/private/genomes/solanum_lycopersicum/annotation
 244 </feature>
 245 #
 246 cview_db_backend    cxgn
 247
 248 #how to find blast stuff
 249 blast_path                ""
 250 blast_db_path             /export/prod/blast/databases/current
 251 preselected_blastdb       224
 252 jbrowse_path              /jbrowse_solgenomics/?data=data/json
 253
 254
 255 #bin directory used by cluster nodes
 256 cluster_shared_bindir /export/prod/bin
 257 #
 258 #the shared temp directory used by cluster nodes
 259 cluster_shared_tempdir    /export/prod/tmp
 260 gbs_temp_data  /export/prod/public
 261
 262 #
 263 #how verbose we want the warnings to be in the apache error log
 264 verbose_warnings          1
 265 #
 266 # Insitu file locations
 267 insitu_fullsize_dir       /export/prod/public/images/insitu/processed
 268 insitu_fullsize_url       /export/images/insitu/processed
 269 insitu_display_dir        /export/prod/public/images/insitu/display
 270 insitu_display_url        /export/images/insitu/display
 271 insitu_input_dir          /export/prod/public/images/insitu/incoming
 272 #
 273 #path to our production_ftp site
 274 ftpsite_root              /export/prod/public
 275 ftpsite_url               ftp://ftp.solgenomics.net
 276 #path to the pucebaboon temperature sensor file:
 277 pucebaboon_file        /export/prod/public/digitemp.out
 278 #
 279 #path for archving uploaded files
 280 archive_path     /export/prod/sgn_archive
 281
 282 #site overall identifier prefix used for site specific data
 283 #such as stocks, unignes (yet to be implemented) and other datatypes
 284 #for example, uploading barcode phenotyping data will not work without this key (see L<CXGN::Stock::StockBarcode> )
 285 identifier_prefix   SGN
 286
 287 #default genotyping protocol to use:
 288 default_genotyping_protocol undefined(set this in sgn_local.conf)
 289
 290 genotyping_server_host NULL
 291 genotyping_server_username NULL
 292 genotyping_server_password NULL
 293 genotyping_server_token NULL
 294
 295 #HIDAP Shiny Server Support
 296 hidap_enabled    0
 297
 298 #BrAPI params
 299 supportedCrop    Cassava
 300 brapi_require_login 0
 301
 302 #Expression Atlas Connection
 303 has_expression_atlas    0
 304 expression_atlas_url    0
 305
 306 #Homepage controller customization
 307 homepage_display_phenotype_uploads 0
 308
 309 #ODK Services
 310 odk_crossing_data_service_name NULL
 311 odk_crossing_data_service_url https://ona.io
 312 odk_crossing_data_service_username ONAUSER
 313 odk_crossing_data_service_password ONAPASS
 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