sgn_test.conf

   1 # Database configs
   2 dbhost breedbase_db
   3 dbname db
   4 dbuser postgres
   5 dbpass postgres
   6
   7 # Server configuration
   8 production_server 0
   9 debug 1
  10 main_production_site_url http://localhost
  11
  12 # Species options
  13 supportedCrop   Cassava
  14 preferred_species Manihot esculenta
  15
  16 # Ontology options
  17 composable_cvs trait,attribute,tod,toy
  18 composable_cvs_allowed_combinations Image|trait+attribute+tod+toy
  19 composable_cvterm_delimiter |
  20 composable_cvterm_format concise
  21 composable_tod_root_cvterm "Image Pre-Process Type|ISOL:0000021"
  22 composable_toy_root_cvterm "time of year|TIME:0000005"
  23 trait_ontology_db_name CO
  24 trait_ontology_cv_name cassava_trait
  25 trait_ontology_cvterm_name CGIAR cassava trait ontology
  26 onto_root_namespaces  GO (Gene Ontology), PO (Plant Ontology), SO (Sequence Ontology), PATO (Phenotype and Trait Ontology)
  27 trait_variable_onto_root_namespaces CO (Cassava Ontology), COMP (Composed Variables)
  28 allow_observation_variable_submission_interface 1
  29 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)
  30
  31 project_name "breeDBase"
  32
  33 # Login options
  34 disable_login 0
  35 default_login_janedoe 0
  36 require_login 0
  37
  38 # BrAPI options
  39 brapi_require_login 1
  40 brapi_GET any
  41 brapi_POST any
  42 brapi_PUT any
  43 brapi_OPTIONS any
  44
  45 # for drone stuff
  46 python_executable /usr/bin/python3
  47 python_executable_maskrcnn_env /usr/bin/python3
  48
  49 # slurm config
  50 backend Slurm
  51
  52 # web server user
  53 www_user www-data
  54 www_group www-data
  55
  56 # Directory configs
  57 clear_tempfiles_on_restart  1
  58 rootpath /home/production/cxgn
  59 basepath /home/production/cxgn/sgn
  60 homepage_files_dir        /home/production/cxgn/sgn/static/
  61 static_datasets_path      /home/production/SGN_data/public
  62 image_dir                 images/image_files
  63 cluster_shared_tempdir  /tmp/production/SGN-site/
  64 solgs_dir /home/production/tmp/solgs/__USERNAME__
  65 vigs_db_path             /export/prod/blast/databases/current/vigs/
  66 vigs_default_db          Nicotiana_benthamiana_v0.4.4
  67 trial_download_logfile /tmp/production/trial_download_log
  68 archive_path /home/production/archive
  69 image_path images/image_files_test
  70 tempfiles_base /home/production/tmp/breedbase-site
  71 static_content_url  /static_content
  72 static_content_path /home/production/public/static_content
  73 cache_file_path /home/production/cache
  74 r_qtl_temp_path /home/production/tmp/solqtl___USERNAME__
  75 submit_dir                /home/production/public/submit-uploads
  76 blast_path                ""
  77 blast_db_path             /home/production/blast/databases/current
  78 ftpsite_root              /home/production/public
  79 jbrowse_path              /jbrowse_cassavabase/?data=data/json
  80
  81 # Genotyping server options
  82 genotyping_facilities None,Cornell IGD,DArT,Intertek,BGI
  83 genotyping_server_token
  84 genotyping_server_host https://ordering-testing.diversityarrays.com
  85 genotyping_server_username NULL
  86 genotyping_server_password NULL
  87 default_genotyping_protocol GBS ApeKI genotyping v4
  88
  89 <Controller::Cview>
  90     cview_default_map_id 1
  91 </Controller::Cview>
  92 cview_db_backend Cassava
  93
  94 #Homepage controller customization
  95 homepage_display_phenotype_uploads 0
  96
  97
  98 solyc_conversion_files /home/production/solcyc_conversion_files/tomato_unigenes_solyc_conversion_annotated.txt
  99
 100 <View::Mason>
 101 #   add_comp_root /home/production/cxgn/sweetpotatobase/mason
 102 #   add_comp_root /home/production/cannabase/mason
 103 #    add_comp_root /home/production/cxgn/cassava/mason
 104 #   add_comp_root /home/production/cxgn/nelsonlab/mason
 105 #   add_comp_root /home/production/cxgn/cassbase/mason
 106 #   add_comp_root /home/production/cxgn/musabase/mason
 107 #   add_comp_root /home/production/cxgn/yambase/mason
 108 #   add_comp_root /home/production/cxgn/citrusgreening/mason
 109 </View::Mason>
 110
 111 <DatabaseConnection sgn_test>
 112   dsn dbi:Pg:host=localhost;dbname=cxgn
 113   user web_usr
 114   password postgres
 115   search_path public
 116   search_path sgn
 117   search_path annotation
 118   search_path genomic
 119   search_path insitu
 120   search_path metadata
 121   search_path pheno_population
 122   search_path phenome
 123   search_path physical
 124   search_path tomato_gff
 125   search_path biosource
 126   search_path gem
 127 </DatabaseConnection>
 128
 129 order_properties Quantity,Comments
 130 order_properties_dialog Quantity,Comments
 131
 132 ##ODK Services
 133 ##odk_crossing_data_service_name NULL
 134 ##odk_crossing_data_service_url https://ona.io
 135 ##odk_crossing_data_service_username seedtracker
 136 ##odk_crossing_data_service_password Seedtracking101
 137 ##odk_crossing_data_form_name BTractTest
 138 ##odk_crossing_data_test_form_name NULL
 139 ##odk_crossing_data_separate_wishlist_by_location 1
 140 ##odk_phenotyping_data_service_name NULL
 141 ##odk_phenotyping_data_service_url https://bio.smap.com.au
 142 ##odk_phenotyping_data_service_username SMAPUSER
 143 ##odk_phenotyping_data_service_password SMAPPASS
 144 ##crontab_file NULL
 145 ##crontab_log_filepath NULL
 146
 147
 148 noaa_ncdc_access_token DLPxdOEIwKyoiMSuQMRYrtMaiIUpNAwk
 149
 150 identifier_prefix BB
 151
 152 cluster_host breedbase_web