imagebreed_dockerfile/development/sgn_local_docker.conf at master · nickmorales/imagebreed_dockerfile · GitHub

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dbhost breedbase_db
#dbport 5432
dbname empty_fixture
dbuser postgres
dbpass postgres

rootpath /home/production/cxgn
basepath /home/production/cxgn/sgn
hostpath_archive /home/hostarchive

homepage_files_dir        /home/production/public/static_content

trial_download_logfile /home/production/logs/cassava_trial_download_log

authorized_clients_JSON {"fieldbook://":"FieldBook App","https://apps.cipotato.org/hidap_sbase/":"HIDAP","https://imagebreed.org/ImagePipeline/":"Image Analysis Pipeline","https://fieldbook.phenoapps.org/":"fieldbook"}

subscription_model 0
disable_account_confirm 0
disable_login 0
default_login_janedoe 0
require_login 0

#If subscription_model is set to 1, then brapi_require_login is 1
brapi_require_login 1
brapi_GET any
brapi_POST any
brapi_PUT any
brapi_OPTIONS any

www_user www-data
www_group www-data

error_log                 /var/log/sgn/error.log
access_log                /var/log/sgn/access.log

python_executable /home/production/cv/bin/python3
python_executable_maskrcnn_env /home/production/mrcnn/bin/python3

preferred_species Manihot esculenta

clear_tempfiles_on_restart  1

production_server 0
image_dir /images/image_files_test
image_path /home/production/public/images/image_files_test
cluster_shared_tempdir /home/production/tmp
tempfiles_base /home/production/tmp/breedbase-site
static_datasets_path /home/production/public
static_content_url  /static_content
static_content_path /home/production/public/static_content

main_production_site_url http://localhost:7080

noaa_ncdc_access_token DLPxdOEIwKyoiMSuQMRYrtMaiIUpNAwk

enable_opendronemap 0
opendronemap_max_processes 1
drone_imagery_allow_resize 1
drone_imagery_max_standard_processes 3

# github token for contact form
github_access_token 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

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 "time of day|TIME:0000001"
composable_tod_root_cvterm "Image Pre-Process Type|ISOL:0000021"
composable_toy_root_cvterm "time of year|TIME:0000005"
#composable_gen_root_cvterm "generation|TIME:0000072"
allow_observation_variable_submission_interface 1

#trait_ontology_db_name CO
#onto_root_namespaces  GO (Gene Ontology), PO (Plant Ontology), SO (Sequence Ontology), PATO (Phenotype and Trait Ontology), G2F (G2F Variables), COMP (Composed Variables)
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), ALF (Alfalfa)

#Homepage controller customization
homepage_display_phenotype_uploads 0

# jbrowse path
jbrowse_path              /jbrowse_cassavabase/?data=data/json

#path for archving uploaded files
archive_path    /home/production/archive/breedbase/
image_analysis_log    /home/production/archive/image_analysis.log

default_genotyping_protocol "genoprot1"
#Dosage key to use, can be DS for ALT, DR for REF
genotyping_protocol_dosage_key  DS

identifier_prefix BB
project_name "ImageBreed"
cview_db_backend Cassava

# slurm config
backend Slurm
cluster_host breedbase_web
cache_file_path /home/production/cache

solgs_dir        /home/production/tmp/solgs/__USERNAME__
trait_ontology_db_name CO_334

<Controller::Cview>
        cview_default_map_id 1
</Controller::Cview>

submit_dir                /home/production/public/submit-uploads

blast_path                ""
blast_db_path             /home/production/blast/databases/current

# path to our production_ftp site
#
ftpsite_root              /home/production/public

<View::Mason>
       add_comp_root /home/production/cxgn/imagesol/mason
</View::Mason>

<DatabaseConnection sgn_test>
  dsn dbi:Pg:host=breedbase_db;dbname=cxgn
  user postgres
  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>