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