ConfigurationKeys
All configuration keys are available in sgn.conf with their defaults. Do not change any values in that file, as it is git controlled. Instead, change the value in sgn_local.conf, or add the key there with the new value. Values in sgn_local.conf supersede values specified in sgn.conf. sgn_local.conf is not controlled in the default git repo.
#is this a production server?
| key name | explanation | typical values | comments |
|---|---|---|---|
| dbhost | the host for the database | localhost | |
| dbname | the name of the database | fixture | |
| dbuser | web_usr | the name of the postgres database user | usually either web_usr or postgres
|
| dbpass | XYZ | the postgres database password for the dbuser | |
| production_server | is this a production server? | 0 (not a production server), 1 (production server) | production servers do not send out emails for example |
rootpath |
the file path to the cxgn folder | /home/production/cxgn/ |
|
basepath |
the file path to the sgn folder | /home/vagrant/cxgn/sgn |
|
personalized_homepage |
display the personalized homepage | 1 |
|
show_transplanting_date |
whether the transplanting date is shown in the trial creation/edit dialogs and trial info | 0 = hide; 1 = show | |
python_executable |
location of the python executable | /usr/bin/python3.5 |
used for drone data analysis |
python_executable_maskrcnn_env |
locaction of python executable for maskrcnn | /usr/bin/python3.5 |
|
exclude_phenotype_outliers |
whether phenotype outliers should be excluded. DEPRECATED | 0 = include; 1 = exclude | |
image_analysis_services |
the config for automated image analysis services | ``` { "necrosis" : { "server_endpoint" : "http://unet.mcrops.org/api/", "image_type_name" : "image_analysis_necrosis_solomon_nsumba", "description" : "Necrosis Analysis, Makerere University", "service_traits" : { "CBSDpct | CO_334:0002078" : "Cassava" } }, "whitefly_count" : { "server_endpoint" : "http://18.216.149.204/home/api2/", "image_type_name" : "image_analysis_white_fly_count_solomon_nsumba", "description": "Whitefly count, Makarere University" }, "count_contours" : { "image_type_name" : "image_analysis_contours", "trait_name" : "count_contours", "script" : "GetContours.py", "input_image" : "image_path", "outfile_image" : "outfile_path", "results_outfile" : "results_outfile_path", "description" : "Count Contours" }, "largest_contour_percent" : { "image_type_name" : "image_analysis_largest_contour", "trait_name" : "percent_largest_contour", "script" : "GetLargestContour.py", "input_image" : "image_path", "outfile_image" : "outfile_path", "results_outfile" : "results_outfile_path", "description" : "Largest Contour Percent" }, "count_sift" : { "image_type_name" : "image_analysis_sift", "trait_name" : "count_sift", "script" : "ImageProcess/CalculatePhenotypeSift.py", "input_image" : "image_paths", "outfile_image" : "outfile_paths", "results_outfile" : "results_outfile_path", "description" : "SIFT analysis" } }``` |
composable_cvs |
which CVs can be post composed | trait,object,tod,toy,unit,method,experiment_treatment |
|
composable_cvs_allowed_combinations |
which combinations of CVs are allowed | ```Agronomic | trait+toy,Metabolic|trait+object+tod+toy+unit+method``` |
composable_cvterm_delimiter |
the delimiter used to separate different cvterms in composed terms | | | |
composable_cvterm_format |
the composable cvterm format, either concise or | concise | |
composable_variables |
display only variable terms in the post composing tool | 1 | |
composable_tod_root_cvterm |
the root term for the time of day ontology | "time of day|TIME:0000001" | |
composable_toy_root_cvterm |
the root term for the time of year ontology | "time of year|TIME:0000005" | |
composable_gen_root_cvterm |
the generation ontology root term | "generation | TIME:0000072" |
composable_evt_root_cvterm |
the event root term | "event | TIME:0000477" |
composable_validation_check_name |
0 | ||
allow_observation_variable_submission_interface |
whether the observation variable submission interface should be displayed | 0 |
|
trait_ontology_db_name |
the db name of the trait ontology DEPRECATED (should be specified in cvprop table) | SP |
|
trait_ontology_cv_name |
the cv name of the trait ontology DEPRECATED (should be specified in cvprop table) | solanaceae_trait |
|
trait_ontology_cvterm_name |
the name of the root term of the trait ontology | Solanaceae trait ontology |
|
| #For displaying ontologies in Ontology Browser | |||
onto_root_namespaces |
the db names followed by a description in parentheses for the ontologies to be displayed in the ontology browser | GO (Gene Ontology), PO (Plant Ontology), SO (Sequence Ontology), PATO (Phenotype and Trait Ontology), SP (Solanaceae Ontology), UO (Units), CASSTISS (Cass tissues) |
|
allow_trait_edits |
whether variable attribute edits should be allowed | 1 = yes, 0 = no | |
allow_treatment_edits |
whether treatment edits should be allowed | 1 = yes, 0 = no | |
| # Marker Metadata Trait Categories |
Set the DB:Accession of the root term of the ontology used to define trait categories for marker metadata
marker_metadata_trait_ontology_root
The DB:Accession of the root term of the ontology used to define the Seedlot Maintenance categories, events, and values
seedlot_maintenance_event_ontology_root
seedlot_maintenance_info_cvterms
#default_seedlot_material_type seed
project_name SGN
user_registration_join_breeding_programs 0 # when enabled, a new user can choose which breeding programs to join during registration user_registration_admin_confirmation 0 # when enabled, the new user confirmation message will be sent to the address(es) below instead of the user user_registration_admin_confirmation_email # a comma-separated list of email addresses to send new user confirmation messages to, when the above is enabled disable_login 0 default_login_janedoe 0 require_login 0
report_engine phenotype_properties_check
brapi_require_login 1 brapi_observation_units_require_login 1 brapi_observations_require_login 1 brapi_post_variables 0 brapi_put_variables 0 brapi_images_require_login 1 brapi_variables_require_login 1 brapi_lists_require_login 1 #brapi_default_user admin #brapi_default_user_role curator
brapi_treatments_no_management_factor 1 brapi_GET any brapi_POST submitter,curator brapi_PUT submitter,curator brapi_OPTIONS any brapi_include_CO_xref 1 brapi_ou_order_plot_num 0
allow_repeat_measures 0
#export trait names as synonyms (1) or the original trait name (0) fieldbook_trait_synonym 1
list_trait_require_id 1
backend Slurm cache_file_path /home/production/volume/cache job_finish_log /home/production/volume/logs/job_finish.log
crossing prediction tool - should the sex of the plants be taken into account? (for diecieous plants such as Yam)
plant_sex_variable_name "Plant sex estimation 0-4"
preferred_species
www_user USERNAME www_group GROUPNAME
clear_tempfiles_on_restart 1
show_grafting_interface 0 graft_separator_string "on"
solqtl /export/prod/tmp/solqtl/USERNAME
dbsearchpath sgn dbsearchpath public dbsearchpath annotation dbsearchpath genomic dbsearchpath insitu dbsearchpath metadata dbsearchpath pheno_population dbsearchpath phenome dbsearchpath physical dbsearchpath tomato_gff dbsearchpath biosource dbsearchpath gem dbsearchpath sgn_people
#password set_this_please dsn dbi:Pg:host=localhost;dbname=cxgn user 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 search_path sgn_peopleController::Cview cview_default_map_id 9 </Controller::Cview>
##Github access token used for contact form posting of issues github_access_token NULL
##NOAA National Climatic Data Center Access token noaa_ncdc_access_token NULL
#captcha_private_key 6Lc__9YSAAAAANcTczARhRnZRkKmzWjnhipyqI6f #captcha_public_key 6Lc__9YSAAAAAH2ODL2FlR8jKa2Ms9i9d_0ziBWr
static_datasets_url /data static_datasets_path /export/prod/public
static_content_url /static_content static_content_path /export/prod/public/sgn_static_content homepage_files_dir /export/prod/public/sgn_static_content/homepage
Controller::CGI cgi_dir path_to(cgi-bin) </Controller::CGI>
Controller::Genomes::Tomato bac_publish_subdir tomato_genome/bacs </Controller::Genomes::Tomato>
Plugin::SmartURI disposition host-header # application-wide uri_class URI::SmartURI # by default </Plugin::SmartURI>
View::Email::ErrorEmail content_type text/plain to sgn-bugs@solgenomics.net from sgn-bugs@solgenomics.net charset utf-8 dump_skip_class Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet DBIx::Class::Row HTML::Mason::Interp </View::Email::ErrorEmail>
admin_email sgn-feedback@solgenomics.net feedback_email sgn-feedback@solgenomics.net bugs_email sgn-bugs@solgenomics.net email sgn-feedback@solgenomics.net contact_form_email contactform@solgenomics.net cluster_job_email cluster-jobs@solgenomics.net tokn_email scp78@cornell.edu disable_emails 0
smtp_server smtp_layer ssl smtp_auth AUTO smtp_port smtp_login smtp_pass smtp_from
main_production_site_url http://solgenomics.net
#is there a system message text file somewhere we should be displaying? system_message_file HOME/system_message.txt
#tempfiles_base
tempfiles_base ""
#web_cluster_queue
web_cluster_queue batch
#is this a mirror of SGN, or the real thing? is_mirror 0
cosii_files /export/cosii2
error_log /var/log/sgn-site/error.log access_log /var/log/sgn-site/access.log rewrite_log /var/log/sgn-site/rewrite.log blast_log /export/prod/tmp/blast/blast.log image_analysis_log /tmp/image_analysis.log
hmmsearch_location hmmsearch intron_finder_database /export/prod/public/intron_finder_database
trace_path /export/prod/public/chromatograms image_dir /images/image_files image_path /export/prod/public/images tempfiles_subdir /static/documents/tempfiles submit_dir /data/shared/submit-uploads programs_subdir /programs documents_subdir /documents conf_subdir /conf support_data_subdir /support_data
#stock tempfiles (for downloading phenotype and genotype raw data) stock_tempfiles /static/documents/tempfiles/stock #weblogo tempfiles for motifs finder tools
tmp_weblogo_path /static/documents/tempfiles/ tempfiles_base_motifs_finder /home/production/tmp cluster_motifs_finder /home/production/cluster/bin
#currently our cookies encrypt stuff, so this is just a random string to use to do that cookie_encryption_key bo9yie2JeeVee6ouAhch9aomeesieJ3iShae8aa8
genefamily_dir /export/prod/private/genomes/genefamily/ genefamily_format Orthomcl # or orthofinder
stock properties that should be displayed and allowed to be edited in the "additional information" section and can be used in the accession file upload
editable_stock_props variety,released_variety_name,donor,donor institute,donor PUI,country of origin,state,institute code,institute name,biological status of accession code,notes,accession number,PUI,seed source,type of germplasm storage code,acquisition date,organization,location_code,ploidy_level,genome_structure,ncbi_taxonomy_id,transgenic,introgression_parent,introgression_backcross_parent,introgression_map_version,introgression_chromosome,introgression_start_position_bp,introgression_end_position_bp,number_of_insertions,GenbankRecord
editable_stock_props_definitions released_variety_name:offical variety name of the accession or stock,location_code:location code(s) for the accession,ploidy:a number(s) indicating the ploidy (e.g. 2 for diploid or 3 for triploid),genome_structure:genome structure(s) for accession which take into account ploidy and ancestral genome info e.g. AAA or AB,variety:variety(s) can be defined as a group of individuals or plants having similar traits that can be reproduced true to type from generation to generation,donor:the accession_name(s) of the donor accession and should be used in conjunction with donor institute and donor PUI,donor institute:the institute(s) of the donor accession(s),donor PUI:the permanent unique identifier(s) of the donor accession,country of origin:the country(s) of origin,state:the state(s) of origin,institute code: the institute code(s) of origin,institute name:the institute name(s) of origin,biological status of accession code:code(s) indicating the state of accession,notes:free text for notes,accession number:accession number(s) for accession from germplasm bank,PUI:permanent unique identifier(s) of the accession,seed source:origin(s) of seed source,type of germplasm storage code:code(s) indicating the type of germplasm storage,acquisition date:date(s) of acquisition YYYYMMDD for accession,transgenic:indicates if accession is transgenic. Please indicate 1 if transgenic and empty if otherwise.,introgression_parent:if the accession you are adding has an introgression that originated from one of the parents you can specify the parent here,introgression_backcross_parent:the backcross parent for introducing an introgression into the accession being added,introgression_map_version:the map version for identifying the start and stop position of the introgression. e.g. AGPv2,introgression_chromosome:the chromosome number that the introgression is on,introgression_start_position_bp:the start position of the introgression in base pairs,introgression_end_position_bp:the end position of the introgression in base pairs,number_of_insertions:number of transgene insertions in a transgenic plant,organization:the name(s) of the organization(s) which use this accession e.g. NARO,IITA
editable_vector_props Strain,CloningOrganism,InherentMarker,Backbone,SelectionMarker,CassetteName,VectorType,Gene,Promotors,Terminators,GenbankRecord,PlantAntibioticResistantMarker,BacterialResistantMarker
cross_properties Tag Number,Pollination Date,Number of Bags,Number of Flowers,Number of Fruits,Number of Seeds
##Cross properties for yambase ##cross_properties Number of Flowers,Pollination Date,Harvest Date,Number of Seeds Harvested,Days to Maturity,Seed Extraction Date,Number of Seeds Extracted,Number of Viable Seeds,Number of Nonviable Seeds, Days from Harvest to Extraction
##Cross properties for musabase ##cross_properties First Pollination Date,Repeat Pollination Date,Harvest Date,Seed Extraction Date,Number of Seeds Extracted,Embryo Rescue Good Seeds,Embryo Rescue Bad Seeds,Embryo Rescue Total Seeds,Embryo Rescue Date,Subculture Date,Subcultures Count,Subcultures Multiplication Number,Rooting Date,Rooting Plantlet,Germinating After 2 Weeks Date,Active Germinating After 2 Weeks,Germinating Afte 8 Weeks Date,Active Germinating After 8 Weeks,Screenhouse Transfer Date,Hardening Date
cross_additional_info female_focus_trait,male_focus_trait,female_source_trial,male_source_trial cross_additional_info_header Female Focus Trait,Male Focus Trait,Female Source Trial,Male Source Trial
genotyping_facilities None,Cornell IGD,DArT,Intertek,IBRC Japan,BGI
sampling_facilities In-lab,Cornell IGD,DArT,Intertek,IBRC Japan,BGI
management_factor_types Fertilizer,Fungicide,Irrigation,Drought,Herbicide,Weeding,Pruning,Hormone treatment,Light treatment
design_types Completely Randomized,Complete Block,Resolvable Row-Column,Doubly-Resolvable Row-Column,Un-Replicated Diagonal Design, Augmented Row-Column,Alpha Lattice,Lattice,Augmented,Modified Augmented Design,Nursery/Greenhouse,Split Plot,Strip Plot,Partially Replicated,Westcott
trial_activities Started Phenotyping, Phenotyping Completed, Data Cleaning Completed, Data Analysis Completed
properties for ordering system (required 2 sets of order properties: order_properties and order_properties_dialog)
customized dropdown menu can be included in the order_properties_dialog. Dropdown menu can be linked with each property by using ":"
#order_properties Quantity,Facility,Scientist,Required by Date,Experiment Name,Experiment Type #order_properties_dialog Quantity,Facility:green house:growth chamber,Scientist,Required by Date,Experiment Name,Experiment Type:seed production:experimentation
###for setting up a single step submission use the following: #ordering_type single_step ##two steps (adding to your cart first) is by default
order_properties Quantity,Comments order_properties_dialog Quantity,Comments
##for connecting orders with tracking activity project tracking_order_activity 0
##for connecting transformation with tracking activity project tracking_transformation 0
tracking_activities subculture_count,rooted_count,hardened_count tracking_activities_header Subculture Count,Rooted Count,Hardened Count
tracking_transformation_info coculture_date,number_of_transformants tracking_transformation_info_header Co-culture Date, Number of Transformants
tracking_tissue_culture_info subculture_count,rooted_count,hardened_count tracking_tissue_culture_info_header Subculture Count,Rooted Count,Hardened Count
##Whether obsoleted accessions are allowed to include in new trials allow_obsoleted_accessions 0
enabled 1 enabled 1 # # default GBrowse2 configuration, for a Debian gbrowse2 installation enabled 1 perl_inc /usr/local/share/website/gbrowse/lib/perl5 tmp_dir /usr/local/share/website/tmp/gbrowse cgi_url /gbrowse/bin static_url /gbrowse/static run_mode fastcgi cgi_bin /usr/lib/cgi-bin/gbrowse static_dir /usr/local/share/website/gbrowse/htdocs # # default ITAG config enabled 1 pipeline_base /export/shared/tomato_genome/itagpipeline/itag releases_base /export/prod/private/genomes/solanum_lycopersicum/annotation # cview_db_backend cxgn#how to find blast stuff blast_path "" blast_db_path /export/prod/blast/databases/current preselected_blastdb 224 jbrowse_path /jbrowse_solgenomics/?data=data/json
Set the the Blast DB (by species and reference genome) used for getting the marker flanking sequence
flanking_sequence_blast_db
#bin directory used by cluster nodes cluster_shared_bindir /export/prod/bin
#the shared temp directory used by cluster nodes cluster_shared_tempdir /export/prod/tmp gbs_temp_data /export/prod/public
cluster_host ""
#how verbose we want the warnings to be in the apache error log verbose_warnings 1
insitu_fullsize_dir /export/prod/public/images/insitu/processed insitu_fullsize_url /export/images/insitu/processed insitu_display_dir /export/prod/public/images/insitu/display insitu_display_url /export/images/insitu/display insitu_input_dir /export/prod/public/images/insitu/incoming
#path to our production_ftp site ftpsite_root /export/prod/public ftpsite_url ftp://ftp.solgenomics.net #path to the pucebaboon temperature sensor file: pucebaboon_file /export/prod/public/digitemp.out
#path for archving uploaded files archive_path /export/prod/sgn_archive
#path for Cache::File system. used by CXGN::Dataset::Cache
#site overall identifier prefix used for site specific data #such as stocks, unignes (yet to be implemented) and other datatypes #for example, uploading barcode phenotyping data will not work without this key (see LCXGN::Stock::StockBarcode ) identifier_prefix SGN
#default genotyping protocol to use: default_genotyping_protocol undefined(set this in sgn_local.conf)
genotyping_server_host NULL genotyping_server_username NULL genotyping_server_password NULL genotyping_server_token NULL
#HIDAP Shiny Server Support hidap_enabled 0
#BrAPI params supportedCrop Cassava
#Expression Atlas Connection has_expression_atlas 0 expression_atlas_url 0
#Sampling trial tissue types sample_tissue_types leaf,root,stem,seed,fruit,tuber
#Homepage controller customization homepage_display_phenotype_uploads 0
ordering_service_name NULL ordering_service_url https://ona.io ordering_service_username ONAUSER ordering_service_password ONAPASS
#ODK Services odk_crossing_data_service_name NULL odk_crossing_data_service_url https://ona.io odk_crossing_data_service_username ONAUSER odk_crossing_data_service_password ONAPASS odk_crossing_data_test_form_name NULL odk_crossing_data_separate_wishlist_by_location 0 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
#Transcriptomics protocol options library_method_options 3RNA-Seq, Small RNA-seq, Poly(A)-Enriched Methods (mRNA-Seq), Total RNA-Seq (ribo-depleted), Single-Cell RNA-Seq (scRNA-Seq), Iso-Seq, Spatial Transcriptomics , Extracellular RNA-Seq instrument_model_options NovaSeq X Plus, NovaSeq X, NovaSeq 6000, NextSeq 2000, NextSeq 1000, NextSeq 500, NextSeq 550, MiSeq, HiSeq 2500, HiSeq 3000/4000, HiSeq X, Sequel IIe, REvio, PacBio RSII, PromethION 48, PromethION 24, GridION X5, MinION Mk1C, MinION Mk1B,Flongle, Chromium iX, Chromium X, Visium, DNBSEQ-T7, DNBSEQ-G400 (MGISEQ-2000), DNBSEQ-G50 (MGISEQ-200), Evercode, GEXSCOPE, Ion Proton, Ion S5, Ion S5 XL layout_options Single-end, Paired-end, mate-paire, single-molecule, single-cell, long-read, exon capture mapping_software_options HISAT2, STAR, TopHat2, Bowtie2, Subjunc, GATK, MapSplice sequencing_platform_options Illumina, PacBio, Oxford Nanopore Technologies, 10C genomics Chromium, BGI/MGI, Element Biosciences (AVITI), Parse Biiosciences(Evercode), Singleron (GEXSCOPE), Slide-seq, MERFISH/seqFISH, Thermo Fisher Ion Torrent , BGI Small RNA-seq, na_extraction_method_options RNeasy Mini Kit, RNeasy Plus Mini Kit, RNeasy Plant Mini Kit, Thermo Fisher GeneJET RNA Purification Kit, TRIzol (Invitrogen), Zymo Quick-RNA Plant Kit, Zymo Quick-RNA Fungal/Bacterial Kit, Nucleospin RNA Plant Kit, Biozym RNAprep Plant Kit, CTAB Method, LiCl Method, TRIzol, Dynabeads mRNA DIRECT Kit , Dynabeads mRNA Purification Kit, Beckman Coulter Agencourt RNAClean XP Kit, Nucleospin RNA Kit
#Authorized Clients for SSO
authorized_clients_JSON {"TEST://":"TEST","fieldbook://":"Field Book App","https://apps.cipotato.org/hidap_sbase/":"HIDAP","https://phenoapps.org/field-book":"Field Book App","https://fieldbook.phenoapps.org/": "Field Book App","https://phenoapps.org/coordinate":"Coordinate App","https://phenoapps.org/intercross":"Intercross App","https://snpsnapp.breedbase.org":"snpsnapp","https://climmob.net":"ClimMob", "https://synonyms.triticeaetoolbox.org":"BrAPI Synonym Search Tool"}
simsearch_datadir /home/production/simsearch_data
version sgn-311.0-236 version_updated 2021-12-23T19:04:41Z
# Create OAuth client ID in the cloud console: https://console.cloud.google.com/apis/credentials
client_id .apps.googleusercontent.com # [REQUIRED] Client ID in google (XXX.apps.googleusercontent.com)
well_known_url https://accounts.google.com/.well-known/openid-configuration # [REQUIRED] Well Known Configuration
well_known_url https:///auth/realms//.well-known/openid-configuration # [REQUIRED] Well Known Configuration
root@b8da7160b875:~/cxgn/sgn#
