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 composable_cvs trait, toy
  14 allowed_combinations "trait+toy"
  15
  16 project_name SGN
  17
  18 disable_login 0
  19
  20 # the species that should be preselected in a list of species
  21 #
  22 preferred_species
  23
  24 # who is the web server user for chowning and emailing.  need to set
  25 # these manually under Apache mod_perl for example, because the server
  26 # runs under a different user than when it starts.
  27 www_user                 __USERNAME__
  28 www_group                __GROUPNAME__
  29
  30 # when true, server removes its tempfiles when the app is started
  31 clear_tempfiles_on_restart  1
  32
  33 solqtl /export/prod/tmp/solqtl/__USERNAME__
  34 ##### other config variables #####
  35
  36 dbsearchpath   sgn
  37 dbsearchpath   public
  38 dbsearchpath   annotation
  39 dbsearchpath   genomic
  40 dbsearchpath   insitu
  41 dbsearchpath   metadata
  42 dbsearchpath   pheno_population
  43 dbsearchpath   phenome
  44 dbsearchpath   physical
  45 dbsearchpath   tomato_gff
  46 dbsearchpath   biosource
  47 dbsearchpath   gem
  48 dbsearchpath   sgn_people
  49
  50 <DatabaseConnection sgn_test>
  51         #password   set_this_please
  52         dsn   dbi:Pg:host=localhost;dbname=cxgn
  53         user   postgres
  54         search_path   public
  55         search_path   sgn
  56         search_path   annotation
  57         search_path   genomic
  58         search_path   insitu
  59         search_path   metadata
  60         search_path   pheno_population
  61         search_path   phenome
  62         search_path   physical
  63         search_path   tomato_gff
  64         search_path   biosource
  65         search_path   gem
  66         search_path   sgn_people
  67 </DatabaseConnection>
  68
  69 ### Cview configuration parameters
  70 <Controller::Cview>
  71         cview_default_map_id 9
  72 </Controller::Cview>
  73
  74 ## captcha keys for the production site
  75 #captcha_private_key  6Lc__9YSAAAAANcTczARhRnZRkKmzWjnhipyqI6f
  76 #captcha_public_key   6Lc__9YSAAAAAH2ODL2FlR8jKa2Ms9i9d_0ziBWr
  77
  78 ### backcompat variables for the various static content types
  79 # relative URL and absolute path for static datasets
  80 static_datasets_url       /data
  81 static_datasets_path      /export/prod/public
  82
  83 # relative URL and absoluate path for static site content
  84 static_content_url        /static_content
  85 static_content_path       /export/prod/public/sgn_static_content
  86 homepage_files_dir        /export/prod/public/sgn_static_content/homepage
  87
  88 # this needs to be here rather than in the CGI controller itself to
  89 # work around a bug in all but the most recent
  90 # Catalyst::Controller::CGIBin
  91 <Controller::CGI>
  92     cgi_dir   __path_to(cgi-bin)__
  93 </Controller::CGI>
  94
  95 <Controller::Genomes::Tomato>
  96    bac_publish_subdir tomato_genome/bacs
  97 </Controller::Genomes::Tomato>
  98
  99 <Plugin::SmartURI>
 100                disposition host-header   # application-wide
 101                uri_class   URI::SmartURI # by default
 102 </Plugin::SmartURI>
 103
 104
 105 <View::Email::ErrorEmail>
 106     <default>
 107         content_type  text/plain
 108         to            sgn-bugs@solgenomics.net
 109         from          sgn-bugs@solgenomics.net
 110         charset       utf-8
 111     </default>
 112     dump_skip_class   Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet  DBIx::Class::Row  HTML::Mason::Interp
 113 </View::Email::ErrorEmail>
 114
 115 # should we send emails, if we are a production server? this can be
 116 # used to turn off emails if we are being bombarded.
 117 admin_email              sgn-feedback@solgenomics.net
 118 feedback_email           sgn-feedback@solgenomics.net
 119 bugs_email               sgn-bugs@solgenomics.net
 120 email                    sgn-feedback@solgenomics.net
 121 contact_form_email       contactform@solgenomics.net
 122 tokn_email               scp78@cornell.edu
 123 disable_emails           0
 124
 125 # URL of the canonical, main production site
 126 main_production_site_url  http://solgenomics.net
 127
 128 #is there a system message text file somewhere we should be displaying?
 129 system_message_file       __HOME__/system_message.txt
 130 # defaults to /tmp/<user>/SGN-site
 131 #tempfiles_base
 132
 133
 134 tempfiles_base            ""
 135 #
 136
 137 # where to run cluster jobs - nothing means "batch" queue
 138 #web_cluster_queue
 139
 140
 141 # where to run cluster jobs
 142 web_cluster_queue        batch
 143
 144
 145 #is this a mirror of SGN, or the real thing?
 146 is_mirror                 0
 147 #
 148 # how to find cosii_files for markerinfo.pl
 149 cosii_files               /export/cosii2
 150 #
 151 # log files, ABSOLUTE PATHS
 152 error_log                 /var/log/sgn-site/error.log
 153 access_log                /var/log/sgn-site/access.log
 154 rewrite_log               /var/log/sgn-site/rewrite.log
 155 blast_log                 /export/prod/tmp/blast/blast.log
 156 #
 157 # paths to stuff
 158 hmmsearch_location        hmmsearch
 159 intron_finder_database    /export/prod/public/intron_finder_database
 160 #
 161 trace_path                /export/prod/public/chromatograms
 162 image_dir                 /images/image_files
 163 image_path                /export/prod/public/images
 164 tempfiles_subdir          /static/documents/tempfiles
 165 submit_dir                /data/shared/submit-uploads
 166 programs_subdir           /programs
 167 documents_subdir          /documents
 168 conf_subdir               /conf
 169 support_data_subdir       /support_data
 170 #
 171 #stock tempfiles (for downloading phenotype and genotype raw data)
 172 stock_tempfiles           /static/documents/tempfiles/stock
 173 #
 174 #currently our cookies encrypt stuff, so this is just a random string to use to do that
 175 cookie_encryption_key     bo9yie2JeeVee6ouAhch9aomeesieJ3iShae8aa8
 176 #
 177 # where the genefamily info is stored
 178 genefamily_dir            /export/prod/private/genomes/genefamily/
 179 #
 180 # the right ontology db name for the trait search
 181 trait_ontology_db_name SP
 182 onto_root_namespaces  GO (Gene Ontology), PO (Plant Ontology), SO (Sequence Ontology), PATO (Phenotype and Trait Ontology), SP (Solanaceae Ontology)
 183 ##
 184
 185 ##
 186 # stock properties that should be displayed and allowed to be edited in the "additional information" section
 187 #editable_stock_props variety,donor,donor institute,country of origin,state,adaptation,notes
 188 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
 189 ##
 190
 191 <feature SGN::Feature::FeaturePages>
 192     enabled      1
 193 </feature>
 194 <feature SGN::Feature::LocusPages>
 195     enabled      1
 196 </feature>
 197 #
 198 # default GBrowse2 configuration, for a Debian gbrowse2 installation
 199 <feature SGN::Feature::GBrowse2>
 200     enabled      1
 201     perl_inc     /usr/local/share/website/gbrowse/lib/perl5
 202     tmp_dir      /usr/local/share/website/tmp/gbrowse
 203     cgi_url      /gbrowse/bin
 204     static_url   /gbrowse/static
 205     run_mode     fastcgi
 206     cgi_bin      /usr/lib/cgi-bin/gbrowse
 207     static_dir   /usr/local/share/website/gbrowse/htdocs
 208 </feature>
 209 #
 210 # default ITAG config
 211 <feature SGN::Feature::ITAG>
 212     enabled         1
 213     pipeline_base   /export/shared/tomato_genome/itagpipeline/itag
 214     releases_base   /export/prod/private/genomes/solanum_lycopersicum/annotation
 215 </feature>
 216 #
 217 cview_db_backend    cxgn
 218
 219
 220 #how to find blast stuff
 221 blast_path                ""
 222 blast_db_path             /export/prod/blast/databases/current
 223 preselected_blastdb       224
 224 jbrowse_path              /jbrowse_solgenomics/?data=data/json
 225
 226
 227 #bin directory used by cluster nodes
 228 cluster_shared_bindir /export/prod/bin
 229 #
 230 #the shared temp directory used by cluster nodes
 231 cluster_shared_tempdir    /export/prod/tmp
 232 gbs_temp_data  /export/prod/public
 233
 234 #
 235 #how verbose we want the warnings to be in the apache error log
 236 verbose_warnings          1
 237 #
 238 # Insitu file locations
 239 insitu_fullsize_dir       /export/prod/public/images/insitu/processed
 240 insitu_fullsize_url       /export/images/insitu/processed
 241 insitu_display_dir        /export/prod/public/images/insitu/display
 242 insitu_display_url        /export/images/insitu/display
 243 insitu_input_dir          /export/prod/public/images/insitu/incoming
 244 #
 245 #path to our production_ftp site
 246 ftpsite_root              /export/prod/public
 247 ftpsite_url               ftp://ftp.solgenomics.net
 248 #path to the pucebaboon temperature sensor file:
 249 pucebaboon_file        /export/prod/public/digitemp.out
 250 #
 251 #path for archving uploaded files
 252 archive_path     /export/prod/sgn_archive
 253
 254 #site overall identifier prefix used for site specific data
 255 #such as stocks, unignes (yet to be implemented) and other datatypes
 256 #for example, uploading barcode phenotyping data will not work without this key (see L<CXGN::Stock::StockBarcode> )
 257 identifier_prefix   SGN
 258
 259 #default genotyping protocol to use:
 260 default_genotyping_protocol undefined(set this in sgn_local.conf)
 261
 262 #HIDAP Shiny Server Support
 263 hidap_enabled    0
 264
 265 #BrAPI params
 266 supportedCrop    Cassava
 267
 268 #Expression Atlas Connection
 269 has_expression_atlas    0
 270 expression_atlas_url    0
 271
 272 #Homepage controller customization
 273 homepage_display_phenotype_uploads 0