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
  10 dbuser   web_usr
  11 #dbpass   set_this_here
  12
  13 vigs_tool_blast_datasets 148 149 196 69
  14
  15 project_name SGN
  16
  17 disable_login 0
  18
  19 # who is the web server user for chowning and emailing.  need to set
  20 # these manually under Apache mod_perl for example, because the server
  21 # runs under a different user than when it starts.
  22 www_user                 __USERNAME__
  23 www_group                __GROUPNAME__
  24
  25 # when true, server removes its tempfiles when the app is started
  26 clear_tempfiles_on_restart  1
  27
  28 r_qtl_temp_path /data/prod/tmp/solqtl___USERNAME__
  29
  30 ##### other config variables #####
  31
  32 dbsearchpath   sgn
  33 dbsearchpath   public
  34 dbsearchpath   annotation
  35 dbsearchpath   genomic
  36 dbsearchpath   insitu
  37 dbsearchpath   metadata
  38 dbsearchpath   pheno_population
  39 dbsearchpath   phenome
  40 dbsearchpath   physical
  41 dbsearchpath   tomato_gff
  42 dbsearchpath   biosource
  43 dbsearchpath   gem
  44
  45 <DatabaseConnection sgn_test>
  46         #password   set_this_please
  47         dsn   dbi:Pg:host=localhost;dbname=cxgn
  48         user   postgres
  49         search_path   public
  50         search_path   sgn
  51         search_path   annotation
  52         search_path   genomic
  53         search_path   insitu
  54         search_path   metadata
  55         search_path   pheno_population
  56         search_path   phenome
  57         search_path   physical
  58         search_path   tomato_gff
  59         search_path   biosource
  60         search_path   gem
  61 </DatabaseConnection>
  62
  63 ### Cview configuration parameters
  64 <Controller::Cview>
  65         cview_default_map_id 9
  66 </Controller::Cview>
  67
  68 ## captcha keys for the production site
  69 captcha_private_key  6Lc__9YSAAAAANcTczARhRnZRkKmzWjnhipyqI6f
  70 captcha_public_key   6Lc__9YSAAAAAH2ODL2FlR8jKa2Ms9i9d_0ziBWr
  71
  72 contact_form_human_question 2+3
  73 contact_form_human_answer   5
  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      /data/prod/public
  79
  80 # relative URL and absoluate path for static site content
  81 static_content_url        /static_content
  82 static_content_path       /data/prod/public/sgn_static_content
  83 homepage_files_dir        /data/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 <View::Email::ErrorEmail>
  97     <default>
  98         content_type  text/plain
  99         to            sgn-bugs@solgenomics.net
 100         from          sgn-bugs@solgenomics.net
 101         charset       utf-8
 102     </default>
 103     dump_skip_class   Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet  DBIx::Class::Row  HTML::Mason::Interp
 104 </View::Email::ErrorEmail>
 105
 106 # should we send emails, if we are a production server? this can be
 107 # used to turn off emails if we are being bombarded.
 108 admin_email              sgn-feedback@solgenomics.net
 109 feedback_email           sgn-feedback@solgenomics.net
 110 bugs_email               sgn-bugs@solgenomics.net
 111 email                    sgn-feedback@solgenomics.net
 112 disable_emails           0
 113
 114 # URL of the canonical, main production site
 115 main_production_site_url  http://solgenomics.net
 116
 117 #is there a system message text file somewhere we should be displaying?
 118 system_message_file       __HOME__/system_message.txt
 119 # defaults to /tmp/<user>/SGN-site
 120 #tempfiles_base
 121
 122
 123 tempfiles_base            ""
 124 #
 125
 126 # where to run cluster jobs - nothing means "batch" queue
 127 #web_cluster_queue
 128
 129
 130 # where to run cluster jobs
 131 web_cluster_queue        batch
 132
 133
 134 #is this a mirror of SGN, or the real thing?
 135 is_mirror                 0
 136 #
 137 # how to find cosii_files for markerinfo.pl
 138 cosii_files               /data/cosii2
 139 #
 140 # log files, ABSOLUTE PATHS
 141 error_log                 /var/log/sgn-site/error.log
 142 access_log                /var/log/sgn-site/access.log
 143 rewrite_log               /var/log/sgn-site/rewrite.log
 144 #
 145 # paths to stuff
 146 hmmsearch_location        hmmsearch
 147 intron_finder_database    /data/prod/public/intron_finder_database
 148 #
 149 trace_path                /data/prod/public/chromatograms
 150 image_dir                 /images/image_files
 151 image_path                /data/prod/public/images
 152 tempfiles_subdir          /static/documents/tempfiles
 153 submit_dir                /data/shared/submit-uploads
 154 programs_subdir           /programs
 155 documents_subdir          /documents
 156 conf_subdir               /conf
 157 support_data_subdir       /support_data
 158 #
 159 #stock tempfiles (for downloading phenotype and genotype raw data)
 160 stock_tempfiles           /static/documents/tempfiles/stock
 161 #
 162 #currently our cookies encrypt stuff, so this is just a random string to use to do that
 163 cookie_encryption_key     bo9yie2JeeVee6ouAhch9aomeesieJ3iShae8aa8
 164 #
 165 # where the genefamily info is stored
 166 genefamily_dir            /data/prod/private/genomes/genefamily/
 167 #
 168 # the right ontology db name for the trait search
 169 trait_ontology_db_name SP
 170 onto_root_namespaces  GO (Gene Ontology), PO (Plant Ontology), SO (Sequence Ontology), PATO (Phenotype and Trait Ontology), SP (Solanaceae Ontology)
 171 ##
 172
 173 <feature SGN::Feature::FeaturePages>
 174     enabled      1
 175 </feature>
 176 <feature SGN::Feature::LocusPages>
 177     enabled      1
 178 </feature>
 179 #
 180 # default GBrowse2 configuration, for a Debian gbrowse2 installation
 181 <feature SGN::Feature::GBrowse2>
 182     enabled      1
 183     perl_inc     /usr/share/gbrowse/lib/perl5
 184     tmp_dir      /var/tmp/gbrowse
 185     cgi_url      /gbrowse/bin
 186     static_url   /gbrowse/static
 187     run_mode     fcgi
 188     cgi_bin      /usr/share/gbrowse/cgi-bin
 189     static_dir   /usr/share/gbrowse/htdocs
 190 </feature>
 191 #
 192 # default ITAG config
 193 <feature SGN::Feature::ITAG>
 194     enabled         1
 195     pipeline_base   /data/shared/tomato_genome/itagpipeline/itag
 196     releases_base   /data/prod/private/genomes/solanum_lycopersicum/annotation
 197 </feature>
 198 #
 199 cview_db_backend    cxgn
 200 #
 201 #how to find blast stuff
 202 blast_path                ""
 203 blast_db_path             /data/shared/blast/databases/current
 204
 205 vigs_tool_blast_datasets  148 149 196 69
 206 #
 207 #the shared temp directory used by cluster nodes
 208 cluster_shared_tempdir    /data/prod/tmp
 209 #
 210 #how verbose we want the warnings to be in the apache error log
 211 verbose_warnings          1
 212 #
 213 # Insitu file locations
 214 insitu_fullsize_dir       /data/prod/public/images/insitu/processed
 215 insitu_fullsize_url       /data/images/insitu/processed
 216 insitu_display_dir        /data/prod/public/images/insitu/display
 217 insitu_display_url        /data/images/insitu/display
 218 insitu_input_dir          /data/prod/public/images/insitu/incoming
 219 #
 220 #path to our production_ftp site
 221 ftpsite_root              /data/prod/public
 222 ftpsite_url               ftp://ftp.solgenomics.net
 223 #path to the pucebaboon temperature sensor file:
 224 pucebaboon_file        /data/prod/public/digitemp.out
 225 #
 226 #path for archving uploaded files
 227 archive_path     /data/prod/sgn_archive
 228
 229 #site overall identifier prefix used for site specific data
 230 #such as stocks, unignes (yet to be implemented) and other datatypes
 231 #for example, uploading barcode phenotyping data will not work without this key (see L<CXGN::Stock::StockBarcode> )
 232 identifier_prefix   SGN