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Lukas Mueller edited this page Apr 24, 2026 · 41 revisions

Configuration keys

All configuration keys are available in sgn.conf with their defaults. Do not change any values in that file, as it is git controlled. Instead, change the value in sgn_local.conf, or add the key there with the new value. Values in sgn_local.conf supersede values specified in sgn.conf. sgn_local.conf is not controlled in the default git repo.

#is this a production server?

key name typical value explanation comments
# Database connection
dbhost localhost the host for the database
dbname fixture the name of the database
dbuser web_usr the name of the postgres database user usually either web_usr or postgres
dbpass [REDACTED] the postgres database password for the dbuser
production_server is this a production server? 0 (not a production server), 1 (production server) production servers do not send out emails for example
rootpath the file path to the cxgn folder /home/production/cxgn/
basepath the file path to the sgn folder /home/vagrant/cxgn/sgn
personalized_homepage display the personalized homepage 1
show_transplanting_date whether the transplanting date is shown in the trial creation/edit dialogs and trial info 0 = hide; 1 = show
python_executable location of the python executable /usr/bin/python3.5 used for drone data analysis
python_executable_maskrcnn_env locaction of python executable for maskrcnn /usr/bin/python3.5
exclude_phenotype_outliers whether phenotype outliers should be excluded. DEPRECATED 0 = include; 1 = exclude
image_analysis_services the config for automated image analysis services ``` { "necrosis" : { "server_endpoint" : "http://unet.mcrops.org/api/", "image_type_name" : "image_analysis_necrosis_solomon_nsumba", "description" : "Necrosis Analysis, Makerere University", "service_traits" : { "CBSDpct CO_334:0002078" : "Cassava" } }, "whitefly_count" : { "server_endpoint" : "http://18.216.149.204/home/api2/", "image_type_name" : "image_analysis_white_fly_count_solomon_nsumba", "description": "Whitefly count, Makarere University" }, "count_contours" : { "image_type_name" : "image_analysis_contours", "trait_name" : "count_contours", "script" : "GetContours.py", "input_image" : "image_path", "outfile_image" : "outfile_path", "results_outfile" : "results_outfile_path", "description" : "Count Contours" }, "largest_contour_percent" : { "image_type_name" : "image_analysis_largest_contour", "trait_name" : "percent_largest_contour", "script" : "GetLargestContour.py", "input_image" : "image_path", "outfile_image" : "outfile_path", "results_outfile" : "results_outfile_path", "description" : "Largest Contour Percent" }, "count_sift" : { "image_type_name" : "image_analysis_sift", "trait_name" : "count_sift", "script" : "ImageProcess/CalculatePhenotypeSift.py", "input_image" : "image_paths", "outfile_image" : "outfile_paths", "results_outfile" : "results_outfile_path", "description" : "SIFT analysis" } }```
composable_cvs which CVs can be post composed trait,object,tod,toy,unit,method,experiment_treatment
composable_cvs_allowed_combinations which combinations of CVs are allowed ```Agronomic trait+toy,Metabolic|trait+object+tod+toy+unit+method```
composable_cvterm_delimiter the delimiter used to separate different cvterms in composed terms |
composable_cvterm_format the composable cvterm format, either concise or concise
composable_variables display only variable terms in the post composing tool 1
composable_tod_root_cvterm the root term for the time of day ontology "time of day|TIME:0000001"
composable_toy_root_cvterm the root term for the time of year ontology "time of year|TIME:0000005"
composable_gen_root_cvterm the generation ontology root term "generation TIME:0000072"
composable_evt_root_cvterm the event root term "event TIME:0000477"
composable_validation_check_name 0
allow_observation_variable_submission_interface whether the observation variable submission interface should be displayed 0
trait_ontology_db_name the db name of the trait ontology DEPRECATED (should be specified in cvprop table) SP
trait_ontology_cv_name the cv name of the trait ontology DEPRECATED (should be specified in cvprop table) solanaceae_trait
trait_ontology_cvterm_name the name of the root term of the trait ontology Solanaceae trait ontology
#For displaying ontologies in Ontology Browser
onto_root_namespaces the db names followed by a description in parentheses for the ontologies to be displayed in the ontology browser GO (Gene Ontology), PO (Plant Ontology), SO (Sequence Ontology), PATO (Phenotype and Trait Ontology), SP (Solanaceae Ontology), UO (Units), CASSTISS (Cass tissues)
allow_trait_edits whether variable attribute edits should be allowed 1 = yes, 0 = no
allow_treatment_edits whether treatment edits should be allowed 1 = yes, 0 = no
# Marker Metadata Trait Categories
marker_metadata_trait_ontology_root Set the DB:Accession of the root term of the ontology used to define trait categories for marker metadata
seedlot_maintenance_event_ontology_root Seedlot Maintenance Events
seedlot_maintenance_event_ontology_root SEEDLOT_MAINTENANCE:0000000 The DB:Accession of the root term of the ontology used to define the Seedlot Maintenance categories, events, and values
seedlot_maintenance_info_cvterms 78211,78168 The cvterm_id(s) of event(s) displayed as seedlot information on the record page
default_seedlot_material_type seed, root, clone, plant, tissue culture or gametophyte seedlot material type options
project_name SGN String used on some pages to identify the website
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 fred@sanger.com a comma-separated list of email addresses to send new user confirmation messages to, when the above is enabled
disable_login 0 0 enables all logins; 1 disables all logins
default_login_janedoe 0 default login enabled
require_login 0 all pages required login if set to 1
# Report parameters
report_engine phenotype_properties_check
# BrAPI related
brapi_require_login 1 if BrAPI calls require login
brapi_observation_units_require_login DEPRECATED 1
brapi_observations_require_login DEPRECATED 1
brapi_post_variables DEPRECATED 0
brapi_put_variables DEPRECATED 0
brapi_images_require_login DEPRECATED 1
brapi_variables_require_login DEPRECATED 1
brapi_lists_require_login 1
brapi_default_user admin
brapi_default_user_role DEPRECATED curator should use role of actual default user
brapi_treatments_no_management_factor DEPRECATED 1 temporary feature flag until breedbase is storing treatments properly through brapi
brapi_GET DEPRECATED any
brapi_POST DEPRECATED submitter,curator
brapi_PUT DEPRECATED submitter,curator
brapi_OPTIONS DEPRECATED any
brapi_include_CO_xref 1
brapi_ou_order_plot_num 0
allow_repeat_measures DEPRECATED 0 replaced by repetitive measure interfaces (set on level of each variable)
fieldbook_trait_synonym 1 export trait names as synonyms (1) or the original trait name (0)
list_trait_require_id 1
backend Slurm Cluster backend the only valid option is slurm right now
cache_file _/home/production/volume/cache file path to cache dir
job_finish_log /home/production/volume/logs/job_finish.log
plant_sex_variable_name "Plant sex estimation 0-4" for crossing prediction tool - should the sex of the plants be taken into account? (for diecieous plants such as Yam)
preferred_species Manihot esculenta the species that should be preselected in a list of species
www_user www-data who is the web server user for chowning and emailing. need to set set to USERNAME for current user
www_group www-data the group of the webserver process set to GROUPNAME for group of executing user
clear_tempfiles_on_restart 1 when true, server removes its tempfiles when the app is started
show_grafting_interface 0 show the grafting interface
graft_separator_string "on" the string to connect the rootstock from the scion names, forming the name of the graft
solqtl /export/prod/tmp/solqtl/__USERNAME__
dbsearchpath sgn the search path that will be set in the database. Can be repeated for specifying several schemas
Controller::Cview 
    cview_default_map_id 9

</Controller::Cview>

| the Cview config for the default map |  | 
| ```github_access_token``` | [REDACTED] | Github access token used for contact form posting of issues |  |
| ```noaa_ncdc_access_token``` | [REDACTED] | NOAA National Climatic Data Center Access token | | 
| ```captcha_private_key``` | [REDACTED] |  The captcha private key |  | 
| ```captcha_public_key``` | [REDACTED] |  The captcha public key |   | 
| ```static_datasets_url``` | ```/data```  |  relative URL for static datasets |  |
| ```static_datasets_path``` | ```/export/prod/public``` | absolute path for static datasets |  |
| ```static_content_url``` | ```/static_content``` | relative URL for static site content  |   | 
| ```static_content_path``` | ```/export/prod/public/sgn_static_content``` | absolute path for static site content |  |
| ```homepage_files_dir``` | ```/export/prod/public/sgn_static_content/homepage``` | absoluate path for homepage content |  |
| # 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``` DEPRECATED | ```sgn-feedback@solgenomics.net``` | Deprecated. Users are expected to use the Google Issues linked contact form |  |  
| ```feedback_email``` DEPRECATED | ```sgn-feedback@solgenomics.net``` | Deprecated. Users are expected to use the Google Issues linked contact form |   |
| ```bugs_email``` | ```sgn-bugs@solgenomics.net``` | where error messages are being sent to |  | 
| ```email``` | ```sgn-feedback@solgenomics.net``` |  |   |
| ```contact_form_email``` | ```contactform@solgenomics.net``` | The email that the contact form uses |  | 
| ```cluster_job_email``` | ```cluster-jobs@solgenomics.net``` | This may not be used. Check! |  | 
| ```tokn_email``` | ```scp78@cornell.edu``` | contact email for the tokn sub-site. Review for appropriateness. |  | 
| ```disable_emails``` | ```0``` | 0 = site does not send emails, 1 = it does |  |
| ```smtp_server``` |   |  specifies the mail server to be used |   | 
| ```smtp_layer``` | ```ssl``` | the smtp layer used for communicating the the mail server |  | 
| ```smtp_auth``` | ```AUTO``` | the authorization used with the mail server |  | 
| ```smtp_port``` |   | the port used with the mail server |  | 
| ```smtp_login``` |   | the username associated with the mail server account |  | 
| ```smtp_pass``` |    | the password associated with the mail server account |   |
| ```smtp_from``` |     | the from field to be used with messages |  | 
| ```main_production_site_url``` | ```http://solgenomics.net``` | the URL of the canonical, main production site. Used to construct certain links, such as in the password resetting process |  | 
| ```system_message_file``` | ```__HOME__/system_message.txt``` | file that contains a system message displayed as a system message in the page header |  | 
| ```tempfiles_base``` |  defaults to /tmp/<user>/SGN-site |  |  | 
| ```web_cluster_queue``` | ```batch``` | where to run cluster jobs - nothing means "batch" queue |  |
| ```is_mirror``` | ```0``` | is this a mirror of SGN, or the real thing? | | 
| ```cosii_files``` | ```/export/cosii2``` | where to find cosii_files for markerinfo.pl |  |
| ```error_log``` | ```/var/log/sgn-site/error.log``` | the location of the error log |  |
| ```access_log``` | ```/var/log/sgn-site/access.log``` | the location of the access log |  | 
| ```rewrite_log``` | ```/var/log/sgn-site/rewrite.log``` | the rewrite log. May not be used (Check this) |  | 
| ```blast_log``` | ```/export/prod/tmp/blast/blast.log``` | the blast log. May not be used (check this) |  | 
| ```image_analysis_log``` | ```/tmp/image_analysis.log``` | the image analysis log. |  | 
| ```hmmsearch_location``` | ```hmmsearch``` | location of the hmmsearch tool |  | 
| ```intron_finder_database``` | ```/export/prod/public/intron_finder_database``` | the location of the intron finder database |  |
| ```trace_path``` | ```/export/prod/public/chromatograms``` | where the chromatograms are stored (for Sanger sequences) |  | 
| ```image_dir``` | ```/images/image_files``` | the image subdir |  | 
| ```image_path``` DEPRECATED | ```/export/prod/public/images``` | This is not used. The image path is constructed from 
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/
tempfiles_base_motifs_finder /home/production/tmp
cluster_motifs_finder /home/production/cluster/bin
#
#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,number_of_insertions,GenbankRecord


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,number_of_insertions:number of transgene insertions in a transgenic plant,organization:the name(s) of the organization(s) which use this accession e.g. NARO,IITA


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

##

## 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,Un-Replicated Diagonal Design, 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

##Whether obsoleted accessions are allowed to include in new trials
allow_obsoleted_accessions 0
##

<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

#Expression Atlas Connection
has_expression_atlas    0
expression_atlas_url	0

#Sampling trial tissue types
sample_tissue_types leaf,root,stem,seed,fruit,tuber

#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

#Transcriptomics protocol options
library_method_options 3RNA-Seq, Small RNA-seq, Poly(A)-Enriched Methods (mRNA-Seq), Total RNA-Seq (ribo-depleted), Single-Cell RNA-Seq (scRNA-Seq), Iso-Seq, Spatial Transcriptomics , Extracellular RNA-Seq
instrument_model_options NovaSeq X Plus, NovaSeq X, NovaSeq 6000, NextSeq 2000, NextSeq 1000, NextSeq 500, NextSeq 550, MiSeq, HiSeq 2500, HiSeq 3000/4000, HiSeq X, Sequel IIe, REvio, PacBio RSII, PromethION 48, PromethION 24, GridION X5, MinION Mk1C, MinION Mk1B,Flongle, Chromium iX, Chromium X, Visium, DNBSEQ-T7, DNBSEQ-G400 (MGISEQ-2000), DNBSEQ-G50 (MGISEQ-200), Evercode, GEXSCOPE, Ion Proton, Ion S5, Ion S5 XL
layout_options Single-end, Paired-end, mate-paire, single-molecule, single-cell, long-read, exon capture
mapping_software_options HISAT2, STAR, TopHat2, Bowtie2, Subjunc, GATK, MapSplice
sequencing_platform_options Illumina, PacBio, Oxford Nanopore Technologies, 10C genomics Chromium, BGI/MGI, Element Biosciences (AVITI), Parse Biiosciences(Evercode), Singleron (GEXSCOPE), Slide-seq, MERFISH/seqFISH, Thermo Fisher Ion Torrent , BGI Small RNA-seq,
na_extraction_method_options RNeasy Mini Kit, RNeasy Plus Mini Kit, RNeasy Plant Mini Kit, Thermo Fisher GeneJET RNA Purification Kit, TRIzol (Invitrogen), Zymo Quick-RNA Plant Kit, Zymo Quick-RNA Fungal/Bacterial Kit, Nucleospin RNA Plant Kit, Biozym RNAprep Plant Kit, CTAB Method, LiCl Method, TRIzol, Dynabeads mRNA DIRECT Kit , Dynabeads mRNA Purification Kit, Beckman Coulter Agencourt RNAClean XP Kit, Nucleospin RNA Kit


#Authorized Clients for SSO

authorized_clients_JSON {"TEST://":"TEST","fieldbook://":"Field Book App","https://apps.cipotato.org/hidap_sbase/":"HIDAP","https://phenoapps.org/field-book":"Field Book App","https://fieldbook.phenoapps.org/": "Field Book App","https://phenoapps.org/coordinate":"Coordinate App","https://phenoapps.org/intercross":"Intercross App","https://snpsnapp.breedbase.org":"snpsnapp","https://climmob.net":"ClimMob", "https://synonyms.triticeaetoolbox.org":"BrAPI Synonym Search Tool"}

simsearch_datadir /home/production/simsearch_data

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

# <oidc_client>
#     # Create OAuth client ID in the cloud console: https://console.cloud.google.com/apis/credentials
#     # Authorized JavaScript origins: https://<BREEDBASE DOMAIN>
#     # Authorized redirect URIs: https://<BREEDBASE DOMAIN>/authenticate/oidc/google/callback
#     <google>
#         client_id         <YOUR CLIENT_ID HERE>.apps.googleusercontent.com             # [REQUIRED] Client ID in google (XXX.apps.googleusercontent.com)
#         client_secret     <YOUR CLIENT_SECRET HERE>                                    # [REQUIRED] Client Secret in google
#         well_known_url    https://accounts.google.com/.well-known/openid-configuration # [REQUIRED] Well Known Configuration
#         auto_provision    0                                                            # [OPTIONAL] If email does not exist in database, don't create new user
#     </google>
#
#     <keycloak>
#         client_id              <KEYCLOAK CLIENT ID>                                                            # [REQUIRED] Client ID in keycloak
#         client_secret          <KEYCLOAK CLIENT SECRET>                                                        # [REQUIRED] Client ID in keycloak
#         well_known_url         https://<KEYCLOAK DOMAIN>/auth/realms/<REALM>/.well-known/openid-configuration  # [REQUIRED] Well Known Configuration
#         code_challenge_method  S256                                                                            # [OPTIONAL] PKCE code challenge method
#         auto_provision         1                                                                               # [OPTIONAL] If email does not exist in database, do create new user
#     </keycloak>
# </oidc_client>
root@b8da7160b875:~/cxgn/sgn# 

# 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>

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