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 # External SMTP Server to send emails
 150 smtp_server
 151 smtp_port
 152 smtp_user
 153 smtp_pass
 154 smtp_from
 155
 156 # URL of the canonical, main production site
 157 main_production_site_url  http://solgenomics.net
 158
 159 #is there a system message text file somewhere we should be displaying?
 160 system_message_file       __HOME__/system_message.txt
 161 # defaults to /tmp/<user>/SGN-site
 162 #tempfiles_base
 163
 164
 165 tempfiles_base            ""
 166 #
 167
 168 # where to run cluster jobs - nothing means "batch" queue
 169 #web_cluster_queue
 170
 171
 172 # where to run cluster jobs
 173 web_cluster_queue        batch
 174
 175
 176 #is this a mirror of SGN, or the real thing?
 177 is_mirror                 0
 178 #
 179 # how to find cosii_files for markerinfo.pl
 180 cosii_files               /export/cosii2
 181 #
 182 # log files, ABSOLUTE PATHS
 183 error_log                 /var/log/sgn-site/error.log
 184 access_log                /var/log/sgn-site/access.log
 185 rewrite_log               /var/log/sgn-site/rewrite.log
 186 blast_log                 /export/prod/tmp/blast/blast.log
 187 #
 188 # paths to stuff
 189 hmmsearch_location        hmmsearch
 190 intron_finder_database    /export/prod/public/intron_finder_database
 191 #
 192 trace_path                /export/prod/public/chromatograms
 193 image_dir                 /images/image_files
 194 image_path                /export/prod/public/images
 195 tempfiles_subdir          /static/documents/tempfiles
 196 submit_dir                /data/shared/submit-uploads
 197 programs_subdir           /programs
 198 documents_subdir          /documents
 199 conf_subdir               /conf
 200 support_data_subdir       /support_data
 201 #
 202 #stock tempfiles (for downloading phenotype and genotype raw data)
 203 stock_tempfiles           /static/documents/tempfiles/stock
 204 #
 205 #currently our cookies encrypt stuff, so this is just a random string to use to do that
 206 cookie_encryption_key     bo9yie2JeeVee6ouAhch9aomeesieJ3iShae8aa8
 207 #
 208 # where the genefamily info is stored
 209 genefamily_dir            /export/prod/private/genomes/genefamily/
 210 #
 211
 212 ##
 213 # stock properties that should be displayed and allowed to be edited in the "additional information" section
 214 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
 215 ##
 216
 217 ## Cross properties that should be displayed and allowed to be added to crosses on cross detail page.
 218 ## Cross properties for cassavabase
 219 cross_properties Tag Number,Pollination Date,Number of Bags,Number of Flowers,Number of Fruits,Number of Seeds
 220
 221 ##Cross properties for yambase
 222 ##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
 223
 224 ##Cross properties for musabase
 225 ##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
 226
 227 <feature SGN::Feature::FeaturePages>
 228     enabled      1
 229 </feature>
 230 <feature SGN::Feature::LocusPages>
 231     enabled      1
 232 </feature>
 233 #
 234 # default GBrowse2 configuration, for a Debian gbrowse2 installation
 235 <feature SGN::Feature::GBrowse2>
 236     enabled      1
 237     perl_inc     /usr/local/share/website/gbrowse/lib/perl5
 238     tmp_dir      /usr/local/share/website/tmp/gbrowse
 239     cgi_url      /gbrowse/bin
 240     static_url   /gbrowse/static
 241     run_mode     fastcgi
 242     cgi_bin      /usr/lib/cgi-bin/gbrowse
 243     static_dir   /usr/local/share/website/gbrowse/htdocs
 244 </feature>
 245 #
 246 # default ITAG config
 247 <feature SGN::Feature::ITAG>
 248     enabled         1
 249     pipeline_base   /export/shared/tomato_genome/itagpipeline/itag
 250     releases_base   /export/prod/private/genomes/solanum_lycopersicum/annotation
 251 </feature>
 252 #
 253 cview_db_backend    cxgn
 254
 255 #how to find blast stuff
 256 blast_path                ""
 257 blast_db_path             /export/prod/blast/databases/current
 258 preselected_blastdb       224
 259 jbrowse_path              /jbrowse_solgenomics/?data=data/json
 260
 261
 262 #bin directory used by cluster nodes
 263 cluster_shared_bindir /export/prod/bin
 264 #
 265 #the shared temp directory used by cluster nodes
 266 cluster_shared_tempdir    /export/prod/tmp
 267 gbs_temp_data  /export/prod/public
 268
 269 #
 270 #how verbose we want the warnings to be in the apache error log
 271 verbose_warnings          1
 272 #
 273 # Insitu file locations
 274 insitu_fullsize_dir       /export/prod/public/images/insitu/processed
 275 insitu_fullsize_url       /export/images/insitu/processed
 276 insitu_display_dir        /export/prod/public/images/insitu/display
 277 insitu_display_url        /export/images/insitu/display
 278 insitu_input_dir          /export/prod/public/images/insitu/incoming
 279 #
 280 #path to our production_ftp site
 281 ftpsite_root              /export/prod/public
 282 ftpsite_url               ftp://ftp.solgenomics.net
 283 #path to the pucebaboon temperature sensor file:
 284 pucebaboon_file        /export/prod/public/digitemp.out
 285 #
 286 #path for archving uploaded files
 287 archive_path     /export/prod/sgn_archive
 288
 289 #site overall identifier prefix used for site specific data
 290 #such as stocks, unignes (yet to be implemented) and other datatypes
 291 #for example, uploading barcode phenotyping data will not work without this key (see L<CXGN::Stock::StockBarcode> )
 292 identifier_prefix   SGN
 293
 294 #default genotyping protocol to use:
 295 default_genotyping_protocol undefined(set this in sgn_local.conf)
 296
 297 genotyping_server_host NULL
 298 genotyping_server_username NULL
 299 genotyping_server_password NULL
 300 genotyping_server_token NULL
 301
 302 #HIDAP Shiny Server Support
 303 hidap_enabled    0
 304
 305 #BrAPI params
 306 supportedCrop    Cassava
 307 brapi_require_login 0
 308
 309 #Expression Atlas Connection
 310 has_expression_atlas    0
 311 expression_atlas_url    0
 312
 313 #Homepage controller customization
 314 homepage_display_phenotype_uploads 0
 315
 316 #ODK Services
 317 odk_crossing_data_service_name NULL
 318 odk_crossing_data_service_url https://ona.io
 319 odk_crossing_data_service_username ONAUSER
 320 odk_crossing_data_service_password ONAPASS
 321 odk_crossing_data_test_form_name NULL
 322 odk_crossing_data_separate_wishlist_by_location 0
 323 odk_phenotyping_data_service_name NULL
 324 odk_phenotyping_data_service_url https://bio.smap.com.au
 325 odk_phenotyping_data_service_username SMAPUSER
 326 odk_phenotyping_data_service_password SMAPPASS
 327 crontab_file NULL
 328 crontab_log_filepath NULL