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 | typical value | explanation | comments |
|---|---|---|---|
| Database connection | |||
dbhost |
localhost |
the host for the database | |
dbname |
fixture |
the name of the database | |
dbuser |
web_usr |
the name of the postgres database user | usually either web_usr or postgres
|
dbpass |
[REDACTED] | the postgres database password for the dbuser | |
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 |
|
| Basic Website Configuration | |||
production_server |
is this a production server? | 0 (not a production server), 1 (production server) | production servers do not send out emails for example |
project_name |
SGN | String used on some pages to identify the website | |
main_production_site_url |
http://solgenomics.net |
the URL of the canonical, main production site. Used to construct certain links, such as in the password resetting process | |
is_mirror |
0 |
is this a mirror of SGN, or the real thing? | |
system_message_file |
__HOME__/system_message.txt |
file that contains a system message displayed as a system message in the page header | |
| Logins | |||
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 |
fred@sanger.com | a comma-separated list of email addresses to send new user confirmation messages to, when the above is enabled | |
disable_login |
0 | 0 enables all logins; 1 disables all logins | |
default_login_janedoe |
0 | default login enabled | |
require_login |
0 | all pages required login if set to 1 | |
| File system config | |||
error_log |
/var/log/sgn-site/error.log |
the location of the error log | |
access_log |
/var/log/sgn-site/access.log |
the location of the access log | |
rewrite_log |
/var/log/sgn-site/rewrite.log |
the rewrite log. May not be used (Check this) | |
blast_log |
/export/prod/tmp/blast/blast.log |
the blast log. May not be used (check this) | |
cache_file |
_/home/production/volume/cache
|
file path to cache dir | |
archive_path |
/export/prod/sgn_archive |
every file uploaded to the site should be path archived in this dir, with the original upload filename concatenated with the current time | |
cache_file_path |
/export/prod/sgn_cache |
where cache files can be stored | |
clear_tempfiles_on_restart |
1 | when true, server removes its tempfiles when the app is started | |
image_analysis_log |
/tmp/image_analysis.log |
the image analysis log. | |
hmmsearch_location |
hmmsearch |
location of the hmmsearch tool | |
intron_finder_database |
/export/prod/public/intron_finder_database |
the location of the intron finder database | |
trace_path |
/export/prod/public/chromatograms |
where the chromatograms are stored (for Sanger sequences) | |
image_dir |
/images/image_files |
the image subdir | |
image_path DEPRECATED |
/export/prod/public/images |
This is not used. The image path is constructed from | |
tempfiles_subdir |
/static/documents/tempfiles |
the location of the temp dir, relative to the basepath. | |
static_datasets_url |
/data |
relative URL for static datasets | |
static_datasets_path |
/export/prod/public |
absolute path for static datasets | |
static_content_url |
/static_content |
relative URL for static site content | |
static_content_path |
/export/prod/public/sgn_static_content |
absolute path for static site content | |
homepage_files_dir |
/export/prod/public/sgn_static_content/homepage |
absoluate path for homepage content | |
submit_dir (DEPRECATED) |
/data/shared/submit-uploads |
the submit directory of a deprecated submission system | |
programs_subdir |
/programs |
relative to basepath, where some home grown executables are located | |
documents_subdir |
/documents |
relative to basepath, where documents dir is located. |
|
conf_subdir (DEPRECATED) |
/conf |
old location of a conf dir, replaced by sgn.conf and sgn_local.conf
|
|
cosii_files |
/export/cosii2 |
where to find cosii_files for markerinfo.pl | |
support_data_subdir |
/support_data |
where support data is located. Likely deprecated. | |
stock_tempfiles |
/static/documents/tempfiles/stock |
stock tempfiles (for downloading phenotype and genotype raw data) | |
tmp_weblogo_path |
/static/documents/tempfiles/ |
location of weblogo tempfiles for motifs finder tools | |
tempfiles_base_motifs_finder |
/home/production/tmp |
the temp file dir for the base motifs finder | |
cluster_motifs_finder |
/home/production/cluster/bin |
||
genefamily_dir |
/export/prod/private/genomes/genefamily/ |
where the genefamily info is stored | |
genefamily_format |
Orthomcl |
or orthofinder | |
| Trait and Variable Configuration | |||
allow_repeat_measures DEPRECATED |
0 | replaced by repetitive measure interfaces (set on level of each variable) | |
fieldbook_trait_synonym |
1 | export trait names as synonyms (1) or the original trait name (0) | |
list_trait_require_id |
1 | ||
| Post Composing Configuration | |||
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 | |
| BrAPI configuration | |||
brapi_require_login |
1 | if BrAPI calls require login | |
brapi_observation_units_require_login DEPRECATED |
1 | ||
brapi_observations_require_login DEPRECATED |
1 | ||
brapi_post_variables DEPRECATED |
0 | ||
brapi_put_variables DEPRECATED |
0 | ||
brapi_images_require_login DEPRECATED |
1 | ||
brapi_variables_require_login |
DEPRECATED | 1 | |
brapi_lists_require_login |
1 | ||
brapi_default_user |
admin | ||
brapi_default_user_role DEPRECATED |
curator | should use role of actual default user | |
brapi_treatments_no_management_factor DEPRECATED |
1 | temporary feature flag until breedbase is storing treatments properly through brapi | |
brapi_GET DEPRECATED |
any | ||
brapi_POST DEPRECATED |
submitter,curator | ||
brapi_PUT DEPRECATED |
submitter,curator | ||
brapi_OPTIONS DEPRECATED |
any | ||
brapi_include_CO_xref |
1 | ||
brapi_ou_order_plot_num |
0 |
| cookie_encryption_key | bo9yie2JeeVee6ouAhch9aomeesieJ3iShae8aa8 | currently our cookies encrypt stuff, so this is just a random string to use to do that | may be deprecated |
| 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" } } | for tests: { "plantcv_citrus_app": { "server_endpoint": "http://fake-image-analysis-service/", "image_type_name": "image_analysis_contours", "description": "Citrus Image Analysis (Mocked)", "service_traits": { "Fruit Diameter|INV:0000118": "INV" } } } | |
| show_transplanting_date | whether the transplanting date is shown in the trial creation/edit dialogs and trial info | 0 = hide; 1 = show | |
| Marker Metadata Trait Categories |
| marker_metadata_trait_ontology_root | | Set the DB:Accession of the root term of the ontology used to define trait categories for marker metadata | |
| seedlot_maintenance_event_ontology_root | | Seedlot Maintenance Events | |
| seedlot_maintenance_event_ontology_root | SEEDLOT_MAINTENANCE:0000000 | The DB:Accession of the root term of the ontology used to define the Seedlot Maintenance categories, events, and values | |
| seedlot_maintenance_info_cvterms | 78211,78168 | The cvterm_id(s) of event(s) displayed as seedlot information on the record page
| default_seedlot_material_type | seed, root, clone, plant, tissue culture or gametophyte | seedlot material type options| |
| # Report parameters ||||
| report_engine | phenotype_properties_check | | |
| backend | Slurm | Cluster backend | the only valid option is slurm right now |
| job_finish_log | /home/production/volume/logs/job_finish.log | | |
| plant_sex_variable_name | "Plant sex estimation 0-4" | for crossing prediction tool - should the sex of the plants be taken into account? (for diecieous plants such as Yam) | |
| preferred_species | Manihot esculenta | the species that should be preselected in a list of species | |
| www_user | www-data | who is the web server user for chowning and emailing. need to set | set to USERNAME for current user
| www_group | www-data | the group of the webserver process | set to GROUPNAME for group of executing user |
| show_grafting_interface | 0 | show the grafting interface | |
| graft_separator_string | "on" | the string to connect the rootstock from the scion names, forming the name of the graft | |
| solqtl | /export/prod/tmp/solqtl/__USERNAME__ | | |
| dbsearchpath | sgn | the search path that will be set in the database. Can be repeated for specifying several schemas
| the Cview config for the default map | |
| github_access_token | [REDACTED] | Github access token used for contact form posting of issues | |
| noaa_ncdc_access_token | [REDACTED] | NOAA National Climatic Data Center Access token | |
| captcha_private_key | [REDACTED] | The captcha private key | |
| captcha_public_key | [REDACTED] | The captcha public key | |
| admin_email DEPRECATED | sgn-feedback@solgenomics.net | Deprecated. Users are expected to use the Google Issues linked contact form | |
| feedback_email DEPRECATED | sgn-feedback@solgenomics.net | Deprecated. Users are expected to use the Google Issues linked contact form | |
| bugs_email | sgn-bugs@solgenomics.net | where error messages are being sent to | |
| email | sgn-feedback@solgenomics.net | | |
| contact_form_email | contactform@solgenomics.net | The email that the contact form uses | |
| cluster_job_email | cluster-jobs@solgenomics.net | This may not be used. Check! | |
| tokn_email | scp78@cornell.edu | contact email for the tokn sub-site. Review for appropriateness. | |
| disable_emails | 0 | 0 = site does not send emails, 1 = it does | |
| smtp_server | | specifies the mail server to be used | |
| smtp_layer | ssl | the smtp layer used for communicating the the mail server | |
| smtp_auth | AUTO | the authorization used with the mail server | |
| smtp_port | | the port used with the mail server | |
| smtp_login | | the username associated with the mail server account | |
| smtp_pass | | the password associated with the mail server account | |
| smtp_from | | the from field to be used with messages | |
| tempfiles_base | defaults to /tmp//SGN-site | | |
| web_cluster_queue | batch | where to run cluster jobs - nothing means "batch" queue | |
| 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 | 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_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 | "additional information" section and can be used in the accession file upload | |
| editable_vector_props | Strain,CloningOrganism,InherentMarker,Backbone,SelectionMarker,CassetteName,VectorType,Gene,Promotors,Terminators,GenbankRecord,PlantAntibioticResistantMarker,BacterialResistantMarker | editable vector properties
| cross_properties | Tag Number,Pollination Date,Number of Bags,Number of Flowers,Number of Fruits,Number of Seeds | (cross properties for Cassavabase) | |
| cross_additional_info | female_focus_trait,male_focus_trait,female_source_trial,male_source_trial | cross additional info | |
| cross_additional_info_header | Female Focus Trait,Male Focus Trait,Female Source Trial,Male Source Trial | header info | |
| genotyping_facilities | None,Cornell IGD,DArT,Intertek,IBRC Japan,BGI | which genotype facilities to show for plate submission | |
| sampling_facilities | In-lab,Cornell IGD,DArT,Intertek,IBRC Japan,BGI | sampling facilities to display in genotype submission | |
| management_factor_types (DEPRECATED) | Fertilizer,Fungicide,Irrigation,Drought,Herbicide,Weeding,Pruning,Hormone treatment,Light treatment | Note: Use new treatment interface to create management factors | |
| 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 | available design types when creating a trial | |
| trial_activities | Started Phenotyping, Phenotyping Completed, Data Cleaning Completed, Data Analysis Completed | possible values for trial activities section | |
| order_properties | Quantity,Facility,Scientist,Required by Date,Experiment Name,Experiment Type | properties for ordering system (required 2 sets of order properties: order_properties and order_properties_dialog) | |
| order_properties_dialog | Quantity,Facility:green house:growth chamber,Scientist,Required by Date,Experiment Name,Experiment Type:seed production:experimentation | what's displayed on the order dialog for properties | |
| ordering_type | single_step | for setting up a single step submission | the other value, two steps (adding to your cart first) is the default | |
| order_properties | Quantity,Comments | | |
| order_properties_dialog | Quantity,Comments | | |
| tracking_order_activity | 0 | for connecting orders with tracking activity project | |
| tracking_transformation | 0 | for connecting transformation with tracking activity project | |
| 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 | | |
| allow_obsoleted_accessions | 0 | Whether obsoleted accessions are allowed to include in new trials | |
| cview_db_backend | cxgn | cassava is the other possible value | |
| blast_path | "" | empty string for blast executable in $PATH | |
| blast_db_path | /export/prod/blast/databases/current | where the blast databases are located | |
| preselected_blastdb | 224 | the blast_db_id of the preselected blast database when opening the tools/blast page |
| jbrowse_path | /jbrowse_solgenomics/?data=data/json | where to forward for jbrowse | this is mostly handled by nginx |
| flanking_sequence_blast_db | Triticum aestivum|RefSeq_v1|4,Triticum durum|Triticum durum|5 | the location of the flanking sequence blast dbs | |
| cluster_shared_bindir | /export/prod/bin | the bin directory shared between cluster nodes | |
| cluster_shared_tempdir | /export/prod/tmp | the tmp directory shared between cluster nodes | |
| gbs_temp_data | /export/prod/public | the temp data storage for gbs data (deprecated?) | |
| cluster_host | "" | the domain name or IP address of the cluster host. Cluster commands will be sent there using an ssh connection, which needs ssh keys to be set up. Empty string denotes execution on the local host. | |
| verbose_warnings (DEPRECATED) | 1 | how verbose we want the warnings to be in the apache error log | |
| Insitu file locations |
| insitu_fullsize_dir | /export/prod/public/images/insitu/processed | only used on SGN | |
| insitu_fullsize_url | /export/images/insitu/processed | only used on SGN | |
| insitu_display_dir | /export/prod/public/images/insitu/display | only used on SGN | |
| insitu_display_url | /export/images/insitu/display | only used on SGN | |
| insitu_input_dir | /export/prod/public/images/insitu/incoming | only used on SGN | |
| ftpsite_root | /export/prod/public | path to production_ftp site | |
| ftpsite_url | ftp://ftp.solgenomics.net | url of the ftp site | |
| pucebaboon_file (DEPRECATED) | /export/prod/public/digitemp.out | the path to the output of the temp sensor | |
| identifier_prefix | SGN | a prefix that is appended to certain identifiers | |
| default_genotyping_protocol | undefined | the name of the default genotyping protocol to use | |
| genotyping_server_host (DEPRECATED) | NULL | | |
| genotyping_server_username (DEPRECATED) | NULL | | |
| genotyping_server_password | NULL | | |
| genotyping_server_token | NULL | | |
| hidap_enabled | 0 | HIDAP Shiny Server Support (is this for Musabase?) | |
| supportedCrop | Cassava | the supported crop, can be a comma separated list | |
| has_expression_atlas | 0 | whether this instance has a companion expression atlas | |
| expression_atlas_url | 0 | the URL of the companion expression atlas | |
| sample_tissue_types | leaf,root,stem,seed,fruit,tuber | comma separated list of sample tissue types in sampling trials | |
| homepage_display_phenotype_uploads (DEPRECATED) | 0 | whether to show the recent phenotype uploads | |
| ordering_service_name | NULL | banana ordering system | |
| ordering_service_url | https://ona.io | the ordering URL | |
| ordering_service_username | ONAUSER | | |
| ordering_service_password | ONAPASS | | |
| 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 | | |
| 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 | Transcriptomics protocol options | |
| 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"} | authorized clients for SSO | |
| simsearch_datadir | /home/production/simsearch_data | data dir for the simsearch tool | |
| version (DEPRECATED) | sgn-311.0-236 | the version string of the software | |
| version_updated | 2021-12-23T19:04:41Z | the last update date``` | |
| OIDC Client Configuration | <oidc_client>
#Create OAuth client ID in the cloud console: https://console.cloud.google.com/apis/credentials
#Authorized JavaScript origins: https://
# Authorized redirect URIs: https:///authenticate/oidc/google/callback\n
`client_id .apps.googleusercontent.com` ([REQUIRED] Client ID in google (XXX.apps.googleusercontent.com)
client_secret [REQUIRED] Client Secret in google
`well_known_url https://accounts.google.com/.well-known/openid-configuration` # [REQUIRED] Well Known Configuration
auto_provision 0 email does not exist in database, don't create new user
| | |
well_known_url https:///auth/realms//.well-known/openid-configuration # [REQUIRED] Well Known Configuration
root@b8da7160b875:~/cxgn/sgn#
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>
Controller::Cview cview_default_map_id 9 </Controller::Cview>
<feature SGN::Feature::FeaturePages>
enabled 1
</feature>
<feature SGN::Feature::LocusPages>
enabled 1
</feature>
#
# default GBrowse2 conf##
<feature SGN::Feature::FeaturePages>
enabled 1
</feature>
<feature SGN::Feature::LocusPages>
enabled 1
</feature>
#
# default GBrowse2 configuration, for a Debian gbrowse2 installation
<feature SGN::Feature::GBrowse2>
enabled 1
periguration, for a Debian gbrowse2 installation
<feature SGN::Feature::GBrowse2>
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
</feature>
#
# default ITAG config
<feature SGN::Feature::ITAG>
enabled 1
pipeline_base /export/shared/tomato_genome/itagpipeline/itag
releases_base /export/prod/private/genomes/solanum_lycopersicum/annotation
</feature>
#
##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
