sgn.conf

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

#is this a production server?
production_server         0

#default database connection info
dbhost   localhost
dbname   fixture
dbuser   web_usr
#dbpass   set_this_here

rootpath /home/vagrant/cxgn
basepath /home/vagrant/cxgn/sgn

show_transplanting_date 0

python_executable /home/vagrant/.virtualenvs/cv/bin/python3.5
python_executable_maskrcnn_env /home/vagrant/.virtualenvs/cv/bin/python3.5

exclude_phenotype_outliers 0

composable_cvs trait,object,tod,toy,unit,method
composable_cvs_allowed_combinations Agronomic|trait+toy,Metabolic|trait+object+tod+toy+unit+method
composable_cvterm_delimiter |
composable_cvterm_format concise
composable_tod_root_cvterm "time of day|TIME:0000001"
composable_toy_root_cvterm "time of year|TIME:0000005"
composable_gen_root_cvterm "generation|TIME:0000072"
composable_evt_root_cvterm "event|TIME:0000477"
composable_validation_check_name 0
allow_observation_variable_submission_interface 0
trait_ontology_db_name SP
trait_ontology_cv_name solanaceae_trait
trait_ontology_cvterm_name Solanaceae trait ontology
# For displaying ontologies in Ontology Browser
onto_root_namespaces  GO (Gene Ontology), PO (Plant Ontology), SO (Sequence Ontology), PATO (Phenotype and Trait Ontology), SP (Solanaceae Ontology), UO (Units), CASSTISS (Cass tissues)

# Seedlot Maintenance Events
#
# seedlot_maintenance_event_ontology_root
# The DB:Accession of the root term of the ontology used to define the Seedlot Maintenance categories, events, and values
# seedlot_maintenance_event_ontology_root SEEDLOT_MAINTENANCE:0000000
seedlot_maintenance_event_ontology_root
#
# seedlot_maintenance_info_cvterms
# The cvterm_id(s) of event(s) displayed as seedlot information on the record page
# seedlot_maintenance_info_cvterms 78211,78168
seedlot_maintenance_info_cvterms

project_name SGN

user_registration_join_breeding_programs 0  # when enabled, a new user can choose which breeding programs to join during registration
user_registration_admin_confirmation 0      # when enabled, the new user confirmation message will be sent to the address(es) below instead of the user
user_registration_admin_confirmation_email  # a comma-separated list of email addresses to send new user confirmation messages to, when the above is enabled
disable_login 0
default_login_janedoe 0
require_login 0

brapi_require_login 0
brapi_observation_units_require_login 1
brapi_observations_require_login 1
brapi_post_variables 0
brapi_put_variables  0
brapi_images_require_login 1
brapi_variables_require_login 1
brapi_lists_require_login 1
#brapi_default_user admin
#brapi_default_user_role curator
# temporary feature flag until breedbase is storing treatments properly through brapi
brapi_treatments_no_management_factor 1
brapi_GET any
brapi_POST submitter,curator
brapi_PUT submitter,curator
brapi_OPTIONS any
brapi_include_CO_xref 1
brapi_ou_order_plot_num 0

allow_repeat_measures 0

#export trait names as synonyms (1) or the original trait name (0)
fieldbook_trait_synonym 1

list_trait_require_id 1

# Cluster backend
backend Slurm

# crossing prediction tool - should the sex of the plants be taken into account? (for diecieous plants such as Yam)
# if yes, provide the name of the variable that is used to score the sex of the plant
#
plant_sex_variable_name  "Plant sex estimation 0-4"

# the species that should be preselected in a list of species
#
preferred_species

# 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                 __USERNAME__
www_group                __GROUPNAME__

# when true, server removes its tempfiles when the app is started
clear_tempfiles_on_restart  1

show_grafting_interface 0
graft_separator_string "_on_"

solqtl /export/prod/tmp/solqtl/__USERNAME__
##### 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
        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>

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

##Github access token used for contact form posting of issues
github_access_token NULL

##NOAA National Climatic Data Center Access token
noaa_ncdc_access_token NULL

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

### backcompat variables for the various static content types
# relative URL and absolute path for static datasets
static_datasets_url       /data
static_datasets_path      /export/prod/public

# relative URL and absoluate path for static site content
static_content_url        /static_content
static_content_path       /export/prod/public/sgn_static_content
homepage_files_dir        /export/prod/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>

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

<Plugin::SmartURI>
               disposition host-header   # application-wide
               uri_class   URI::SmartURI # by default
</Plugin::SmartURI>


<View::Email::ErrorEmail>
    <default>
        content_type  text/plain
        to            sgn-bugs@solgenomics.net
        from          sgn-bugs@solgenomics.net
        charset       utf-8
    </default>
    dump_skip_class   Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet  DBIx::Class::Row  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@solgenomics.net
feedback_email           sgn-feedback@solgenomics.net
bugs_email               sgn-bugs@solgenomics.net
email                    sgn-feedback@solgenomics.net
contact_form_email	 contactform@solgenomics.net
cluster_job_email	 cluster-jobs@solgenomics.net
tokn_email		 scp78@cornell.edu
disable_emails           0

# External SMTP Server to send emails
smtp_server
smtp_layer  ssl
smtp_auth   AUTO
smtp_port
smtp_login
smtp_pass
smtp_from

# URL of the canonical, main production site
main_production_site_url  http://solgenomics.net

#is there a system message text file somewhere we should be displaying?
system_message_file       __HOME__/system_message.txt
# defaults to /tmp/<user>/SGN-site
#tempfiles_base


tempfiles_base            ""
#

# where to run cluster jobs - nothing means "batch" queue
#web_cluster_queue


# where to run cluster jobs
web_cluster_queue	 batch


#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
blast_log                 /export/prod/tmp/blast/blast.log
image_analysis_log        /tmp/image_analysis.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_files
image_path                /export/prod/public/images
tempfiles_subdir          /static/documents/tempfiles
submit_dir                /data/shared/submit-uploads
programs_subdir           /programs
documents_subdir          /documents
conf_subdir               /conf
support_data_subdir       /support_data
#
#stock tempfiles (for downloading phenotype and genotype raw data)
stock_tempfiles           /static/documents/tempfiles/stock
#weblogo tempfiles for motifs finder tools
tmp_weblogo_path          /static/documents/tempfiles/
#
#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/
genefamily_format	  Orthomcl   # or orthofinder
#

##
# stock properties that should be displayed and allowed to be edited in the "additional information" section and can be used in the accession file upload
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

editable_vector_props Strain,CloningOrganism,InherentMarker,Backbone,SelectionMarker,CassetteName,VectorType,Gene,Promotors,Terminators

##

## Cross properties that should be displayed and allowed to be added to crosses on cross detail page.
## Cross properties for cassavabase
cross_properties Tag Number,Pollination Date,Number of Bags,Number of Flowers,Number of Fruits,Number of Seeds

##Cross properties for yambase
##cross_properties Number of Flowers,Pollination Date,Harvest Date,Number of Seeds Harvested,Days to Maturity,Seed Extraction Date,Number of Seeds Extracted,Number of Viable Seeds,Number of Nonviable Seeds, Days from Harvest to Extraction

##Cross properties for musabase
##cross_properties First Pollination Date,Repeat Pollination Date,Harvest Date,Seed Extraction Date,Number of Seeds Extracted,Embryo Rescue Good Seeds,Embryo Rescue Bad Seeds,Embryo Rescue Total Seeds,Embryo Rescue Date,Subculture Date,Subcultures Count,Subcultures Multiplication Number,Rooting Date,Rooting Plantlet,Germinating After 2 Weeks Date,Active Germinating After 2 Weeks,Germinating Afte 8 Weeks Date,Active Germinating After 8 Weeks,Screenhouse Transfer Date,Hardening Date


## Cross additional info
cross_additional_info female_focus_trait,male_focus_trait,female_source_trial,male_source_trial
cross_additional_info_header Female Focus Trait,Male Focus Trait,Female Source Trial,Male Source Trial

##
genotyping_facilities None,Cornell IGD,DArT,Intertek,IBRC Japan,BGI
##
##
sampling_facilities In-lab,Cornell IGD,DArT,Intertek,IBRC Japan,BGI
##

##
management_factor_types Fertilizer,Fungicide,Irrigation,Drought,Herbicide,Weeding,Pruning,Hormone treatment,Light treatment
##

##
design_types Completely Randomized,Complete Block,Resolvable Row-Column,Doubly-Resolvable Row-Column,Augmented Row-Column,Alpha Lattice,Lattice,Augmented,Modified Augmented Design,Nursery/Greenhouse,Split Plot,Strip Plot,Partially Replicated,Westcott
##

##
trial_activities Started Phenotyping, Phenotyping Completed, Data Cleaning Completed, Data Analysis Completed
##

### properties for ordering system (required 2 sets of order properties: order_properties and order_properties_dialog)
### customized dropdown menu can be included in the order_properties_dialog. Dropdown menu can be linked with each property by using ":"
### for example Facility and Experiment Type properties have customized dropdown menu:
#order_properties Quantity,Facility,Scientist,Required by Date,Experiment Name,Experiment Type
#order_properties_dialog Quantity,Facility:green house:growth chamber,Scientist,Required by Date,Experiment Name,Experiment Type:seed production:experimentation

###for setting up a single step submission use the following:
#ordering_type single_step
##two steps (adding to your cart first) is by default

order_properties Quantity,Comments
order_properties_dialog Quantity,Comments

##for connecting orders with tracking activity project
tracking_order_activity 0

##for connecting transformation with tracking activity project
tracking_transformation 0

tracking_activities subculture_count,rooted_count,hardened_count
tracking_activities_header Subculture Count,Rooted Count,Hardened Count

tracking_transformation_info coculture_date,number_of_transformants
tracking_transformation_info_header Co-culture Date, Number of Transformants

tracking_tissue_culture_info subculture_count,rooted_count,hardened_count
tracking_tissue_culture_info_header Subculture Count,Rooted Count,Hardened Count

##

<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/local/share/website/gbrowse/lib/perl5
    tmp_dir      /usr/local/share/website/tmp/gbrowse
    cgi_url      /gbrowse/bin
    static_url   /gbrowse/static
    run_mode     fastcgi
    cgi_bin      /usr/lib/cgi-bin/gbrowse
    static_dir   /usr/local/share/website/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>
#
cview_db_backend    cxgn

#how to find blast stuff
blast_path                ""
blast_db_path             /export/prod/blast/databases/current
preselected_blastdb       224
jbrowse_path              /jbrowse_solgenomics/?data=data/json

# Set the the Blast DB (by species and reference genome) used for getting the marker flanking sequence
# flanking_sequence_blast_db  Triticum aestivum|RefSeq_v1|4,Triticum durum|Triticum durum|5
flanking_sequence_blast_db

#bin directory used by cluster nodes
cluster_shared_bindir /export/prod/bin
#
#the shared temp directory used by cluster nodes
cluster_shared_tempdir    /export/prod/tmp
gbs_temp_data  /export/prod/public

cluster_host ""

#
#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
#
#path for archving uploaded files
archive_path     /export/prod/sgn_archive

#path for Cache::File system. used by CXGN::Dataset::Cache
cache_file_path /export/prod/sgn_cache

#site overall identifier prefix used for site specific data
#such as stocks, unignes (yet to be implemented) and other datatypes
#for example, uploading barcode phenotyping data will not work without this key (see L<CXGN::Stock::StockBarcode> )
identifier_prefix   SGN

#default genotyping protocol to use:
default_genotyping_protocol undefined(set this in sgn_local.conf)

genotyping_server_host NULL
genotyping_server_username NULL
genotyping_server_password NULL
genotyping_server_token NULL

#HIDAP Shiny Server Support
hidap_enabled    0

#BrAPI params
supportedCrop    Cassava
brapi_require_login 0

#Expression Atlas Connection
has_expression_atlas    0
expression_atlas_url	0

#Homepage controller customization
homepage_display_phenotype_uploads 0

## banana ordering system
ordering_service_name NULL
ordering_service_url https://ona.io
ordering_service_username ONAUSER
ordering_service_password ONAPASS

#ODK Services
odk_crossing_data_service_name NULL
odk_crossing_data_service_url https://ona.io
odk_crossing_data_service_username ONAUSER
odk_crossing_data_service_password ONAPASS
odk_crossing_data_test_form_name NULL
odk_crossing_data_separate_wishlist_by_location 0
odk_phenotyping_data_service_name NULL
odk_phenotyping_data_service_url https://bio.smap.com.au
odk_phenotyping_data_service_username SMAPUSER
odk_phenotyping_data_service_password SMAPPASS
crontab_file NULL
crontab_log_filepath NULL

#Authorized Clients for SSO
authorized_clients_JSON {"TEST://":"TEST","fieldbook://":"FieldBook App","https://apps.cipotato.org/hidap_sbase/":"HIDAP","https://phenoapps.org/field-book":"fieldbook","https://fieldbook.phenoapps.org/": "fieldbook", "https://climmob.net":"ClimMob"}

simsearch_datadir /home/production/simsearch_data

version sgn-311.0-236
version_updated 2021-12-23T19:04:41Z