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Lukas Mueller edited this page May 4, 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.

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
rootpath /home/production/cxgn/ the file path to the cxgn folder
basepath /home/vagrant/cxgn/sgn the file path to the sgn folder
personalized_homepage 1 display the personalized homepage
Basic Website Configuration
production_server 0 (not a production server), 1 (production server) is this a production server? production servers do not send out emails for example
project_name SGN String used on some pages to identify the website
main_production_site_url https://solgenomics.net the URL of the canonical, main production site. Used to construct certain links, such as in the password resetting process
is_mirror 0 is this a mirror of SGN, or the real thing?
system_message_file __HOME__/system_message.txt file that contains a system message displayed as a system message in the page header
preferred_species Manihot esculenta the species that should be preselected in a list of species
Logins
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
File System and Process Configuration
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
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)
cache_file _/home/production/volume/cache file path to cache dir
archive_path /export/prod/sgn_archive every file uploaded to the site should be path archived in this dir, with the original upload filename concatenated with the current time
cache_file_path /export/prod/sgn_cache where cache files can be stored
clear_tempfiles_on_restart 1 when true, server removes its tempfiles when the app is started
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 the location of the temp dir, relative to the basepath.
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
submit_dir (DEPRECATED) /data/shared/submit-uploads the submit directory of a deprecated submission system
programs_subdir /programs relative to basepath, where some home grown executables are located
documents_subdir /documents relative to basepath, where documents dir is located.
conf_subdir (DEPRECATED) /conf old location of a conf dir, replaced by sgn.conf and sgn_local.conf
cosii_files /export/cosii2 where to find cosii_files for markerinfo.pl
support_data_subdir /support_data where support data is located. Likely deprecated.
stock_tempfiles /static/documents/tempfiles/stock stock tempfiles (for downloading phenotype and genotype raw data)
tmp_weblogo_path /static/documents/tempfiles/ location of weblogo tempfiles for motifs finder tools
tempfiles_base_motifs_finder /home/production/tmp the temp file dir for the base motifs finder
cluster_motifs_finder /home/production/cluster/bin
genefamily_dir /export/prod/private/genomes/genefamily/ where the genefamily info is stored
genefamily_format Orthomcl or orthofinder
Trait and Variable Configuration
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
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
marker_metadata_trait_ontology_root Set the DB:Accession of the root term of the ontology used to define trait categories for marker metadata
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)
Post Composing Configuration
composable_cvs trait,object,tod,toy,unit,method,experiment_treatment which CVs can be post composed
composable_cvs_allowed_combinations `Agronomic trait+toy,Metabolic|trait+object+tod+toy+unit+method` which combinations of CVs are allowed
composable_cvterm_delimiter | the delimiter used to separate different cvterms in composed terms
composable_cvterm_format concise the composable cvterm format, either concise or
composable_variables 1 display only variable terms in the post composing tool
composable_tod_root_cvterm "time of day|TIME:0000001" the root term for the time of day ontology
composable_toy_root_cvterm "time of year|TIME:0000005" the root term for the time of year ontology
composable_gen_root_cvterm `"generation TIME:0000072"` the generation ont rooology root term
composable_evt_root_cvterm `"event TIME:0000477"` the event root term
composable_validation_check_name 0
allow_observation_variable_submission_interface 0 whether the observation variable submission interface should be displayed
trait_ontology_db_name SP the db name of the trait ontology DEPRECATED (should be specified in cvprop table)
trait_ontology_cv_name solanaceae_trait the cv name of the trait ontology DEPRECATED (should be specified in cvprop table)
trait_ontology_cvterm_name Solanaceae trait ontology the name of the root term of the trait ontology
#For displaying ontologies in Ontology Browser
BrAPI configuration
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
Encryption Key Configuration
cookie_encryption_key [REDACTED] currently our cookies encrypt stuff, so this is just a random string to use to do that may be deprecated
Analysis and Cluster Configuration
backend Slurm Cluster backend the only valid option is slurm right now
job_finish_log /home/production/volume/logs/job_finish.log
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" } }```
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
Trial Configuration
show_transplanting_date whether the transplanting date is shown in the trial creation/edit dialogs and trial info 0 = hide; 1 = show
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
Seedlot Configuration
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
Report parameters
report_engine phenotype_properties_check
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
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
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
tempfiles_base defaults to /tmp//SGN-site
web_cluster_queue batch where to run cluster jobs - nothing means "batch" queue
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 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_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 "additional information" section and can be used in the accession file upload
editable_vector_props Strain,CloningOrganism,InherentMarker,Backbone,SelectionMarker,CassetteName,VectorType,Gene,Promotors,Terminators,GenbankRecord,PlantAntibioticResistantMarker,BacterialResistantMarker editable vector properties
cross_properties Tag Number,Pollination Date,Number of Bags,Number of Flowers,Number of Fruits,Number of Seeds (cross properties for Cassavabase)
cross_additional_info female_focus_trait,male_focus_trait,female_source_trial,male_source_trial cross additional info
cross_additional_info_header Female Focus Trait,Male Focus Trait,Female Source Trial,Male Source Trial header info
genotyping_facilities None,Cornell IGD,DArT,Intertek,IBRC Japan,BGI which genotype facilities to show for plate submission
sampling_facilities In-lab,Cornell IGD,DArT,Intertek,IBRC Japan,BGI sampling facilities to display in genotype submission
management_factor_types (DEPRECATED) Fertilizer,Fungicide,Irrigation,Drought,Herbicide,Weeding,Pruning,Hormone treatment,Light treatment Note: Use new treatment interface to create management factors
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 available design types when creating a trial
trial_activities Started Phenotyping, Phenotyping Completed, Data Cleaning Completed, Data Analysis Completed possible values for trial activities section
order_properties Quantity,Facility,Scientist,Required by Date,Experiment Name,Experiment Type properties for ordering system (required 2 sets of order properties: order_properties and order_properties_dialog)
order_properties_dialog Quantity,Facility:green house:growth chamber,Scientist,Required by Date,Experiment Name,Experiment Type:seed production:experimentation what's displayed on the order dialog for properties
ordering_type single_step for setting up a single step submission the other value, two steps (adding to your cart first) is the default
order_properties Quantity,Comments
order_properties_dialog Quantity,Comments
tracking_order_activity 0 for connecting orders with tracking activity project
tracking_transformation 0 for connecting transformation with tracking activity project
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
allow_obsoleted_accessions 0 Whether obsoleted accessions are allowed to include in new trials
cview_db_backend cxgn cassava is the other possible value
blast_path "" empty string for blast executable in $PATH
blast_db_path /export/prod/blast/databases/current where the blast databases are located
preselected_blastdb 224 the blast_db_id of the preselected blast database when opening the tools/blast page
jbrowse_path /jbrowse_solgenomics/?data=data/json where to forward for jbrowse this is mostly handled by nginx
flanking_sequence_blast_db ```Triticum aestivum RefSeq_v1 4,Triticum durum
cluster_shared_bindir /export/prod/bin the bin directory shared between cluster nodes
cluster_shared_tempdir /export/prod/tmp the tmp directory shared between cluster nodes
gbs_temp_data /export/prod/public the temp data storage for gbs data (deprecated?)
cluster_host "" the domain name or IP address of the cluster host. Cluster commands will be sent there using an ssh connection, which needs ssh keys to be set up. Empty string denotes execution on the local host.
verbose_warnings (DEPRECATED) 1 how verbose we want the warnings to be in the apache error log
Insitu file locations
insitu_fullsize_dir /export/prod/public/images/insitu/processed only used on SGN
insitu_fullsize_url /export/images/insitu/processed only used on SGN
insitu_display_dir /export/prod/public/images/insitu/display only used on SGN
insitu_display_url /export/images/insitu/display only used on SGN
insitu_input_dir /export/prod/public/images/insitu/incoming only used on SGN
ftpsite_root /export/prod/public path to production_ftp site
ftpsite_url ftp://ftp.solgenomics.net url of the ftp site
pucebaboon_file (DEPRECATED) /export/prod/public/digitemp.out the path to the output of the temp sensor
identifier_prefix SGN a prefix that is appended to certain identifiers
default_genotyping_protocol undefined the name of the default genotyping protocol to use
genotyping_server_host (DEPRECATED) NULL
genotyping_server_username (DEPRECATED) NULL
genotyping_server_password NULL
genotyping_server_token NULL
hidap_enabled 0 HIDAP Shiny Server Support (is this for Musabase?)
supportedCrop Cassava the supported crop, can be a comma separated list
has_expression_atlas 0 whether this instance has a companion expression atlas
expression_atlas_url 0 the URL of the companion expression atlas
sample_tissue_types leaf,root,stem,seed,fruit,tuber comma separated list of sample tissue types in sampling trials
homepage_display_phenotype_uploads (DEPRECATED) 0 whether to show the recent phenotype uploads
ordering_service_name NULL banana ordering system
ordering_service_url https://ona.io the ordering URL
ordering_service_username ONAUSER
ordering_service_password ONAPASS
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
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``` Transcriptomics protocol options
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"} authorized clients for SSO
simsearch_datadir /home/production/simsearch_data data dir for the simsearch tool
version (DEPRECATED) sgn-311.0-236 the version string of the software
version_updated 2021-12-23T19:04:41Z the last update date```
OIDC Client Configuration <oidc_client>
#Create OAuth client ID in the cloud console: https://console.cloud.google.com/apis/credentials
#Authorized JavaScript origins: https://
# Authorized redirect URIs: https:///authenticate/oidc/google/callback\n
client_id <YOUR CLIENT_ID HERE>.apps.googleusercontent.com ([REQUIRED] Client ID in google (XXX.apps.googleusercontent.com)
client_secret [REQUIRED] Client Secret in google
well_known_url https://accounts.google.com/.well-known/openid-configuration # [REQUIRED] Well Known Configuration
auto_provision 0 email does not exist in database, don't create new user
Keycloak config
client_id <KEYCLOAK CLIENT ID> # [REQUIRED] Client ID in 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

</oidc_client>
Catalyst::Controller::CGIBin <Controller::CGI>
cgi_dir __path_to(cgi-bin)__
</Controller::CGI>
 cgi-bin config
Plugin::SmartURI 
           disposition host-header   # application-wide
           uri_class   URI::SmartURI # by default

</Plugin::SmartURI>

View::Email::ErrorEmail content_type text/plain to sgn-bugs@solgenomics.net from sgn-bugs@solgenomics.net charset utf-8 dump_skip_class Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet DBIx::Class::Row HTML::Mason::Interp </View::Email::ErrorEmail>

Controller::Cview cview_default_map_id 9 </Controller::Cview>

<feature SGN::Feature::FeaturePages>
    enabled      1
</feature>
<feature SGN::Feature::LocusPages>
    enabled      1
</feature>
#
# default GBrowse2 conf##

<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
    periguration, 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>
#

##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

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