2 #### most commonly altered config variables ####
4 #is this a production server?
7 #default database connection info
8 dbhost db.sgn.cornell.edu
13 # who is the web server user for chowning and emailing. need to set
14 # these manually under Apache mod_perl for example, because the server
15 # runs under a different user than when it starts.
17 www_group __GROUPNAME__
19 # when true, server removes its tempfiles when the app is started
20 clear_tempfiles_on_restart 1
22 ##### other config variables #####
26 dbsearchpath annotation
30 dbsearchpath pheno_population
33 dbsearchpath tomato_gff
34 dbsearchpath biosource
37 <DatabaseConnection sgn_test>
38 #password set_this_please
39 dsn dbi:Pg:host=localhost;dbname=cxgn
43 search_path annotation
47 search_path pheno_population
50 search_path tomato_gff
55 ### Cview configuration parameters
57 cview_default_map_id 9
60 ### backcompat variables for the various static content types
61 # relative URL and absolute path for static datasets
62 static_datasets_url /data
63 static_datasets_path /data/prod/public
65 # relative URL and absoluate path for static site content
66 static_content_url /static_content
67 static_content_path /data/prod/public/sgn_static_content
68 homepage_files_dir /data/prod/public/sgn_static_content/homepage
70 # this needs to be here rather than in the CGI controller itself to
71 # work around a bug in all but the most recent
72 # Catalyst::Controller::CGIBin
74 cgi_dir __path_to(cgi-bin)__
77 <View::Email::ErrorEmail>
79 content_type text/plain
80 to sgn-bugs@solgenomics.net
81 from sgn-bugs@solgenomics.net
84 dump_skip_class Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet DBIx::Class::Row HTML::Mason::Interp
85 </View::Email::ErrorEmail>
87 # should we send emails, if we are a production server? this can be
88 # used to turn off emails if we are being bombarded.
89 admin_email sgn-feedback@solgenomics.net
90 feedback_email sgn-feedback@solgenomics.net
91 bugs_email sgn-bugs@solgenomics.net
92 email sgn-feedback@solgenomics.net
95 # URL of the canonical, main production site
96 main_production_site_url http://solgenomics.net
98 #is there a system message text file somewhere we should be displaying?
99 system_message_file __HOME__/system_message.txt
100 # defaults to /tmp/<user>/SGN-site
103 #R qtl tempfiles (must be cluster accessible)
104 r_qtl_temp_path /data/prod/tmp/r_qtl___USERNAME__
106 #allow people to log in?
109 # where to run cluster jobs
112 #is this a mirror of SGN, or the real thing?
115 # how to find cosii_files for markerinfo.pl
116 cosii_files /data/cosii2
118 # log files, ABSOLUTE PATHS
119 error_log /var/log/sgn-site/error.log
120 access_log /var/log/sgn-site/access.log
121 rewrite_log /var/log/sgn-site/rewrite.log
124 hmmsearch_location hmmsearch
125 intron_finder_database /data/prod/public/intron_finder_database
127 trace_path /data/prod/public/chromatograms
128 image_dir /images/image_files
129 image_path /data/prod/public/images
130 tempfiles_subdir /static/documents/tempfiles
131 submit_dir /data/shared/submit-uploads
132 programs_subdir /programs
133 documents_subdir /documents
135 support_data_subdir /support_data
137 #currently our cookies encrypt stuff, so this is just a random string to use to do that
138 cookie_encryption_key bo9yie2JeeVee6ouAhch9aomeesieJ3iShae8aa8
140 # where the genefamily info is stored
141 genefamily_dir /data/prod/private/genomes/genefamily/
143 <feature SGN::Feature::FeaturePages>
146 <feature SGN::Feature::LocusPages>
150 # default GBrowse2 configuration, for a Debian gbrowse2 installation
151 <feature SGN::Feature::GBrowse2>
153 perl_inc /usr/share/gbrowse/lib/perl5
154 tmp_dir /var/tmp/gbrowse
156 static_url /gbrowse/static
158 cgi_bin /usr/share/gbrowse/cgi-bin
159 static_dir /usr/share/gbrowse/htdocs
162 # default ITAG config
163 <feature SGN::Feature::ITAG>
165 pipeline_base /data/shared/tomato_genome/itagpipeline/itag
166 releases_base /data/prod/private/genomes/solanum_lycopersicum/annotation
169 cview_db_backend cxgn
171 #how to find blast stuff
173 blast_db_path /data/shared/blast/databases/current
175 #the shared temp directory used by cluster nodes
176 cluster_shared_tempdir /data/prod/tmp
178 #how verbose we want the warnings to be in the apache error log
181 # Insitu file locations
182 insitu_fullsize_dir /data/prod/public/images/insitu/processed
183 insitu_fullsize_url /data/images/insitu/processed
184 insitu_display_dir /data/prod/public/images/insitu/display
185 insitu_display_url /data/images/insitu/display
186 insitu_input_dir /data/prod/public/images/insitu/incoming
188 #path to our production_ftp site
189 ftpsite_root /data/prod/public
190 ftpsite_url ftp://ftp.solgenomics.net
192 #path to the pucebaboon temperature sensor file:
193 pucebaboon_file /data/prod/public/digitemp.out