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sgn_local.conf
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sgn_local.conf
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dbhost breedbase_db
dbname breedbase
dbuser postgres
dbpass postgres
rootpath /home/production/cxgn
basepath /home/production/cxgn/sgn
#composable_cvs trait,toy # see below
#composable_cvs_allowed_combinations Time Series|trait+toy
homepage_files_dir /home/production/volume/public/static_content
trial_download_logfile /home/production/volume/logs/cassava_trial_download_log
static_datasets_url /data
disable_login 0
brapi_require_login 0
require_login 1
www_user www-data
www_group www-data
contact_form_email info@codingstrand.com
error_log /var/log/sgn/error.log
access_log /var/log/sgn/access.log
python_executable python3
preferred_species Manihot esculenta
production_server 1
image_dir /images/
image_path /home/production/volume/public/images/
cluster_shared_tempdir /home/production/volume/tmp
tempfiles_base /home/production/volume/tmp/breedbase-site
static_datasets_path /home/production/volume/public
static_content_url /static_content
static_content_path /home/production/volume/public/static_content
main_production_site_url https://sample.breedbase.org
# github token for contact form
github_access_token 96d462a40bc3504f4768559e752f7eec16ff2bc1
#Homepage controller customization
homepage_display_phenotype_uploads 0
# jbrowse path
jbrowse_path /jbrowse_cassavabase/?data=data/json
#path for archving uploaded files
archive_path /home/production/volume/archive/breedbase/
default_genotyping_protocol "GBS ApeKI Cassava genome v6_Oct2015"
#default_genotyping_protocol "GBS ApeKI Cassava genome v5"
identifier_prefix BB
project_name Sample
cview_db_backend Cassava
# slurm config
backend Slurm
cluster_host ""
cache_file_path /home/production/volume/cache
solgs_dir /home/production/tmp/solgs/__USERNAME__
trait_ontology_db_name CO_322
trait_cv_name maize_trait
#For display on onto tree
#onto_root_namespaces NO (NCSU_ontology), GO (Gene Ontology), PO (Plant Ontology), SO (Sequence Ontology), PATO (Phenotype and Trait Ontology)
#onto_root_namespaces CO_334 (Cassava Trait Ontology), GO (Gene Ontology), PO (Plant Ontology), SO (Sequence Ontology), PATO (Phenotype and Trait Ontology), DL_001 (Dawson Lab Ontology), TO (Time Ontology)
onto_root_namespaces CO_322 (Maize Trait)
#For display on trait search
trait_variable_onto_root_namespaces CO_322 (Maize Trait), COMP (Composed Variables)
composable_cvs trait,attribute
composable_cvs_allowed_combinations trait+attribute+toy
<Controller::Cview>
cview_default_map_id 1
</Controller::Cview>
r_qtl_temp_path /export/prod/tmp/solqtl___USERNAME__
submit_dir /home/production/public/submit-uploads
blast_path ""
blast_db_path /home/production/volume/blast/databases/current
# path to our production_ftp site
#
ftpsite_root /home/production/volume/public
<View::Mason>
add_comp_root /home/production/cxgn/auburn/mason
</View::Mason>
<DatabaseConnection sgn_test>
dsn dbi:Pg:host=localhost;dbname=cxgn
user postgres
password <your postgres user password>
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
</DatabaseConnection>