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