sgn_local.conf

#### most commonly altered config variables ####

#is this a production server?
production_server         0

#default database connection info
dbhost   breedbase_db
dbname   cxgn_cider
dbuser   postgres
dbpass   postgres

#allow people to log in?
disable_login             0

project_name CiderBase
identifier_prefix CB
# who is the web server user for chowning and emailing.  need to set
# these manually under Apache mod_perl for example, because the server
# runs under a different user than when it starts.
www_user                 www-data
www_group                www-data
basepath		 /home/production/cxgn/sgn
# when true, server removes its tempfiles when the app is started
clear_tempfiles_on_restart  0

# vigs tool settings
###vigs_tool_blast_datasets  155 199 ### old config
vigs_db_path                       /export/prod/blast/databases/current/vigs/
vigs_default_db          Nicotiana_benthamiana_v0.4.4
archive_path             /home/production/archive

solyc_conversion_files /export/prod/public/tomato_genome/id_conversion/tom2_to_solyc_annotated_id40.txt /export/prod/public/tomato_genome/id_conversion/tomato_unigenes_solyc_conversion_annotated.txt

## captcha keys for the production site
#captcha_private_key  6Lc__9YSAAAAANcTczARhRnZRkKmzWjnhipyqI6f 
#captcha_public_key   6Lc__9YSAAAAAH2ODL2FlR8jKa2Ms9i9d_0ziBWr

editable_stock_props variety,released_variety_name,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,ncbi_taxonomy_id,transgenic,introgression_parent,introgression_backcross_parent,introgression_map_version,introgression_chromosome,introgression_start_position_bp,introgression_end_position_bp

editable_stock_props_definitions released_variety_name:offical variety name of the accession or stock,location_code:location code(s) for the accession,ploidy:a number(s) indicating the ploidy (e.g. 2 for diploid or 3 for triploid),genome_structure:genome structure(s) for accession which take into account ploidy and ancestral genome info e.g. AAA or AB,variety:variety(s) can be defined as a group of individuals or plants having similar traits that can be reproduced true to type from generation to generation,donor:the accession_name(s) of the donor accession and should be used in conjunction with donor institute and donor PUI,donor institute:the institute(s) of the donor accession(s),donor PUI:the permanent unique identifier(s) of the donor accession,country of origin:the country(s) of origin,state:the state(s) of origin,institute code: the institute code(s) of origin,institute name:the institute name(s) of origin,biological status of accession code:code(s) indicating the state of accession,notes:free text for notes,accession number:accession number(s) for accession from germplasm bank,PUI:permanent unique identifier(s) of the accession,seed source:origin(s) of seed source,type of germplasm storage code:code(s) indicating the type of germplasm storage,acquisition date:date(s) of acquisition YYYYMMDD for accession,transgenic:indicates if accession is transgenic. Please indicate 1 if transgenic and empty if otherwise.,introgression_parent:if the accession you are adding has an introgression that originated from one of the parents you can specify the parent here,introgression_backcross_parent:the backcross parent for introducing an introgression into the accession being added,introgression_map_version:the map version for identifying the start and stop position of the introgression. e.g. AGPv2,introgression_chromosome:the chromosome number that the introgression is on,introgression_start_position_bp:the start position of the introgression in base pairs,introgression_end_position_bp:the end position of the introgression in base pairs


#github_access_token 96d462a40bc3504f4768559e752f7eec16ff2bc1
github_access_token 70fe80a1fc8b9b4eecd3ca5f870e8d1503db1ced

# captcha keys for the contact form 
captcha_public_key 6LdC_9YSAAAAANoWaNEFqCevO2nB33a-8iFtxeVr
captcha_private_key 6LdC_9YSAAAAAA2gufFSwfFSg0Q2Loji6TYAvjsa

contact_form_human_question 8000+10
contact_form_human_answer 8010

trait_ontology_db_name CIDER
onto_root_namespaces  CIDER (CiderBase Ontology), GO (Gene Ontology), PO (Plant Ontology), SO (Sequence Ontology), PATO (Phenotype and Trait Ontology)

trait_cv_name ciderbase_ontology

##### other config variables #####

dbsearchpath   sgn
dbsearchpath   public
dbsearchpath   annotation
dbsearchpath   genomic
dbsearchpath   insitu
dbsearchpath   metadata
dbsearchpath   pheno_population
dbsearchpath   phenome
dbsearchpath   physical
dbsearchpath   tomato_gff
dbsearchpath   biosource
dbsearchpath   gem
dbsearchpath   sgn_people

<DatabaseConnection sgn_test>
        #password   set_this_please
        dsn   dbi:Pg:host=localhost;dbname=cxgn_test
        user   postgres
        search_path   public
        search_path   sgn
        search_path   annotation
        search_path   genomic
        search_path   insitu
        search_path   metadata
        search_path   pheno_population
        search_path   phenome
        search_path   physical
        search_path   tomato_gff
        search_path   biosource
        search_path   gem
        search_path   sgn_people
</DatabaseConnection>

<Controller::Genomes::Tomato>
   bac_publish_subdir tomato_genome/bacs
</Controller::Genomes::Tomato>


### Cview configuration parameters
<Controller::Cview>
        cview_default_map_id 9
</Controller::Cview>

# URL of the cnaonical, main production site
main_production_site_url  https://solgenomics.net

### backcompat variables for the various static content types
# relative URL and absolute path for static datasets
static_datasets_url       /data
static_datasets_path      /home/production/
#static_datasets_path /tmp/www-data/SGN-site/nonexistent

# relative URL and absoluate path for static site content
static_content_url        /static_content
static_content_path       /home/production/public/sgn_static_content
homepage_files_dir        /home/production/public/sgn_static_content/homepage

# this needs to be here rather than in the CGI controller itself to
# work around a bug in all but the most recent
# Catalyst::Controller::CGIBin
#<Controller::CGI>
#    cgi_dir   __path_to(cgi-bin)__
#</Controller::CGI>

<View::Email::ErrorEmail>
    <default>
        content_type  text/plain
        to            sgn-bugs@rubisco.sgn.cornell.edu
        from          sgn-bugs@rubisco.sgn.cornell.edu
        charset       utf-8
    </default>
    dump_skip_class   Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet  DBIx::Class::Row  HTML::Mason::Interp  SGN Bio::Chado::Schema  HTML::Mason::Interp
</View::Email::ErrorEmail>

# should we send emails, if we are a production server? this can be
# used to turn off emails if we are being bombarded.
admin_email              sgn-feedback@rubisco.sgn.cornell.edu
feedback_email           sgn-feedback@rubisco.sgn.cornell.edu
bugs_email               sgn-bugs@rubisco.sgn.cornell.edu
####contact_form_email	 contactform@solgenomics.net  ###moved to sgn.conf
contact_form_email	 contactform@rubisco.sgn.cornell.edu
email                    contactform@rubisco.sgn.cornell.edu
disable_emails           0
tokn_email               scp78@cornell.edu

#is there a system message text file somewhere we should be displaying?
system_message_file /etc/cxgn/SGN_system_message.txt
      
# defaults to /tmp/<user>/SGN-site
#tempfiles_base            /export/prod/tmp/new-SGN-prod
tempfiles_base    /home/production/tmp

#R qtl tempfiles (must be cluster accessible)
r_qtl_temp_path           /home/production/tmp/solqtl___USERNAME__


# where to run cluster jobs
web_cluster_queue	       

#is this a mirror of SGN, or the real thing?
is_mirror                 0

# how to find cosii_files for markerinfo.pl
cosii_files               /export/cosii2

# log files, ABSOLUTE PATHS
error_log                 /var/log/sgn-site/error.log
access_log                /var/log/sgn-site/access.log
rewrite_log               /var/log/sgn-site/rewrite.log

# paths to stuff
hmmsearch_location        hmmsearch
intron_finder_database    /export/prod/public/intron_finder_database

trace_path                /export/prod/public/chromatograms
image_dir    	          /images/
image_path                /home/production/images
tempfiles_subdir          /static/documents/tempfiles
submit_dir                /export/shared/submit-uploads
programs_subdir           /programs
documents_subdir          /documents
conf_subdir               /conf
support_data_subdir       /support_data
##stock_tempfiles         /static/documents/tempfiles/stock

#currently our cookies encrypt stuff, so this is just a random string to use to do that
cookie_encryption_key     bo9yie2JeeVee6ouAhch9aomeesieJ3iShae8aa8

# where the genefamily info is stored
genefamily_dir            /export/prod/private/genomes/genefamily/

<feature SGN::Feature::FeaturePages>
    enabled      1
</feature>
<feature SGN::Feature::LocusPages>
    enabled      1
</feature>

# default GBrowse2 configuration, for a Debian gbrowse2 installation
#<feature SGN::Feature::GBrowse2>
#    enabled      1
#    perl_inc     /usr/share/gbrowse/lib/perl5
#    tmp_dir      /var/tmp/gbrowse
#    cgi_url      /gbrowse/bin
#    static_url   /gbrowse/static
#    run_mode     fcgi
#    cgi_bin      /usr/share/gbrowse/cgi-bin
#    static_dir   /usr/share/gbrowse/htdocs
#</feature>

# default ITAG config
<feature SGN::Feature::ITAG>
    enabled         1
    pipeline_base   /export/shared/tomato_genome/itagpipeline/itag
    releases_base   /export/prod/private/genomes/solanum_lycopersicum/annotation
</feature>

<View::Mason>
add_comp_root /home/production/uiskin/mason
</View::Mason>


cview_db_backend    cxgn
cluster_host ""
backend Slurm
#how to find blast stuff
blast_path                ""
blast_db_path             /export/prod/blast/databases/current
blast_db_icons 1

#the shared temp directory used by cluster nodes
cluster_shared_tempdir    /home/production/cluster/tmp
#cluster_shared_tempdir    /tmp
cluster_shared_bindir     /home/production/cluster/bin

#how verbose we want the warnings to be in the apache error log
verbose_warnings          1

# Insitu file locations
insitu_fullsize_dir       /export/prod/public/images/insitu/processed
insitu_fullsize_url       /export/images/insitu/processed
insitu_display_dir        /export/prod/public/images/insitu/display
insitu_display_url        /export/images/insitu/display
insitu_input_dir          /export/prod/public/images/insitu/incoming

#path to our production_ftp site
ftpsite_root              /export/prod/public
ftpsite_url               ftp://ftp.solgenomics.net

#path to the pucebaboon temperature sensor file:
pucebaboon_file	       /export/prod/public/digitemp.out

# <feature SGN::Feature::GBrowse2>
#     enabled      1
#     perl_inc     /usr/local/share/website/gbrowse/lib
#     tmp_dir      /usr/local/share/website/gbrowse/tmp/
#     cgi_url      /gbrowse/bin
#     static_url   /gbrowse/static
#     run_mode     fcgi
#     cgi_bin      /usr/local/share/website/gbrowse/cgi-bin
#     static_dir   /usr/local/share/website/gbrowse/htdocs
# </feature>