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