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sgn_test.conf
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sgn_test.conf
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# Database configs
dbhost breedbase_db
dbname db
dbuser postgres
dbpass postgres
# Server configuration
production_server 0
debug 1
main_production_site_url http://localhost
# Species options
supportedCrop Cassava
preferred_species Manihot esculenta
# Ontology options
composable_cvs trait,attribute,tod,toy
composable_cvs_allowed_combinations Image|trait+attribute+tod+toy
composable_cvterm_delimiter |
composable_cvterm_format concise
composable_tod_root_cvterm "Image Pre-Process Type|ISOL:0000021"
composable_toy_root_cvterm "time of year|TIME:0000005"
trait_ontology_db_name CO
trait_ontology_cv_name cassava_trait
trait_ontology_cvterm_name CGIAR cassava trait ontology
onto_root_namespaces GO (Gene Ontology), PO (Plant Ontology), SO (Sequence Ontology), PATO (Phenotype and Trait Ontology)
trait_variable_onto_root_namespaces CO (Cassava Ontology), COMP (Composed Variables)
allow_observation_variable_submission_interface 1
onto_root_namespaces GO (Gene Ontology), PO (Plant Ontology), SO (Sequence Ontology), PATO (Phenotype and Trait Ontology), UO (Units), CASSTISS (Cass tissues), ISOL (Imagesol), G2F (G2F), TIME (Time), SGNSTAT (SGNSTAT)
project_name "breeDBase"
# Login options
disable_login 0
default_login_janedoe 0
require_login 0
# BrAPI options
brapi_require_login 1
brapi_GET any
brapi_POST any
brapi_PUT any
brapi_OPTIONS any
# for drone stuff
python_executable /usr/bin/python3
python_executable_maskrcnn_env /usr/bin/python3
# slurm config
backend Slurm
# web server user
www_user www-data
www_group www-data
# Directory configs
clear_tempfiles_on_restart 1
rootpath /home/production/cxgn
basepath /home/production/cxgn/sgn
homepage_files_dir /home/production/cxgn/sgn/static/
static_datasets_path /home/production/SGN_data/public
image_dir images/image_files
cluster_shared_tempdir /tmp/production/SGN-site/
solgs_dir /home/production/tmp/solgs/__USERNAME__
vigs_db_path /export/prod/blast/databases/current/vigs/
vigs_default_db Nicotiana_benthamiana_v0.4.4
trial_download_logfile /tmp/production/trial_download_log
archive_path /home/production/archive
image_path images/image_files_test
tempfiles_base /home/production/tmp/breedbase-site
static_content_url /static_content
static_content_path /home/production/public/static_content
cache_file_path /home/production/cache
r_qtl_temp_path /home/production/tmp/solqtl___USERNAME__
submit_dir /home/production/public/submit-uploads
blast_path ""
blast_db_path /home/production/blast/databases/current
ftpsite_root /home/production/public
jbrowse_path /jbrowse_cassavabase/?data=data/json
# Genotyping server options
genotyping_facilities None,Cornell IGD,DArT,Intertek,BGI
genotyping_server_token
genotyping_server_host https://ordering-testing.diversityarrays.com
genotyping_server_username NULL
genotyping_server_password NULL
default_genotyping_protocol GBS ApeKI genotyping v4
<Controller::Cview>
cview_default_map_id 1
</Controller::Cview>
cview_db_backend Cassava
#Homepage controller customization
homepage_display_phenotype_uploads 0
solyc_conversion_files /home/production/solcyc_conversion_files/tomato_unigenes_solyc_conversion_annotated.txt
<View::Mason>
# add_comp_root /home/production/cxgn/sweetpotatobase/mason
# add_comp_root /home/production/cannabase/mason
# add_comp_root /home/production/cxgn/cassava/mason
# add_comp_root /home/production/cxgn/nelsonlab/mason
# add_comp_root /home/production/cxgn/cassbase/mason
# add_comp_root /home/production/cxgn/musabase/mason
# add_comp_root /home/production/cxgn/yambase/mason
# add_comp_root /home/production/cxgn/citrusgreening/mason
</View::Mason>
<DatabaseConnection sgn_test>
dsn dbi:Pg:host=localhost;dbname=cxgn
user web_usr
password 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
</DatabaseConnection>
order_properties Quantity,Comments
order_properties_dialog Quantity,Comments
##for connecting orders with tracking activity project
tracking_order_activity 0
##ODK Services
##odk_crossing_data_service_name NULL
##odk_crossing_data_service_url https://ona.io
##odk_crossing_data_service_username seedtracker
##odk_crossing_data_service_password Seedtracking101
##odk_crossing_data_form_name BTractTest
##odk_crossing_data_test_form_name NULL
##odk_crossing_data_separate_wishlist_by_location 1
##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
noaa_ncdc_access_token DLPxdOEIwKyoiMSuQMRYrtMaiIUpNAwk
identifier_prefix BB
cluster_host breedbase_web