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