/
amigo.yaml.tomodachi
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/
amigo.yaml.tomodachi
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---
AMIGO_1X_PUBLIC_CGI_BASE_URL:
comment: The public URL of an available AmiGO 1.x instance for link references.
type: url
value: http://amigo1.geneontology.org/cgi-bin/amigo
AMIGO_API_PORT:
comment: OPTIONAL. The port on which to make available the experimental AmiGO JSON API. Defaults to 6455.
type: number
value: 6455
AMIGO_BALANCER:
comment: 'Mark this AmiGO 2 installation as behind a load balanacer or similar system. The practical effect of this flag is that if AmiGO detects *.error files (usually created by the global-message.pl script), it will return a 503 page signalling any upstream system that the instance is not currently ready.'
type: boolean
value: 1
AMIGO_BETA:
comment: Mark the AmiGO site as BETA (triggers some changes in variables and installed features).
type: boolean
value: 1
AMIGO_BROWSE_FILTER_IDSPACE:
comment: An optional field to filter restrict to globally restrict to a certain ontology during some browsing.
type: string
value: GO
AMIGO_DOWNLOAD_LIMIT:
comment: The download size that AmiGO will default to for the UI.
type: number
value: 100000
AMIGO_DYNAMIC_PATH:
comment: The full path to the location of the perl binaries.
type: directory
value: /home/bbop/local/src/git/amigo/perl/bin
AMIGO_DYNAMIC_URL:
comment: The URL that AMIGO_DYNAMIC_PATH maps to.
type: url
value: http://tomodachi.berkeleybop.org
AMIGO_FOR_GO:
comment: This flag indicates whether or not your AmiGO instance is for the GO, or a more generic instance. If you are trying to run AmiGO locally, probably "1"; if you are trying to have your own AmiGO with different ontologies, data, etc., probably 0.
type: boolean
value: 1
AMIGO_GOOGLE_ANALYTICS_ID:
comment: Google analytics ID. Optional.
type: string
value: 'UA-42073879-1'
AMIGO_LAYOUT_SEARCH:
comment: A whitespace separated list of class IDs to use for live search tabs on the search page.
type: list
value:
- annotation
- ontology
- bioentity
- model_annotation
- noctua_model_meta
- family
- general
- bbop_term_ac
AMIGO_PRIVATE_GOLR_URL:
comment: The (optional) private URL of the GOlr server (including slash); this is the one used for loading. Can be the same as the public URL if you have no proxy or firewall to deal with.
type: url
value: http://localhost:8080/solr/
AMIGO_PUBLIC_GALAXY_URL:
comment: Please enter the public URL of the Galaxy server.
type: url
value: http://galaxy.berkeleybop.org/
AMIGO_PUBLIC_GOLR_BULK_URL:
comment: The public URL of the GOlr bulk download server (including slash); possibly the same as AMIGO_PUBLIC_GOLR_URL.
type: url
value: http://amigo-dev-golr.berkeleybop.org/
AMIGO_PUBLIC_GOLR_URL:
comment: The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.
type: url
value: http://amigo-dev-golr.berkeleybop.org/
AMIGO_PUBLIC_NOCTUA_URL:
comment: The public URL of the Noctua system (including slash).
type: url
value: http://noctua.berkeleybop.org/
AMIGO_ROOT:
comment: 'Unless you are doing something strange, the parent directory of this file.'
type: directory
value: /home/bbop/local/src/git/amigo
AMIGO_ROOT_TERMS:
comment: 'For some widgets, we need to know what root terms you are going to be considering in your ontology. Requires both "id" and "label" to be defined.'
type: json
value:
- id: GO:0008150
label: biological process
- id: GO:0005575
label: cellular component
- id: GO:0003674
label: molecular function
AMIGO_SERVER_NAME:
comment: 'The name by which your AmiGO instance wishes to known--think load balancer or cache situations. If you would rather this information not be reported, leave blank.'
type: string
value: tomodachi
AMIGO_STATIC_PATH:
comment: The full path to a usable static document directory where static and staging are located.
type: directory
value: /home/bbop/local/src/git/amigo/static
AMIGO_STATIC_URL:
comment: The URL for the static content. Can be local or remote.
type: url
value: http://tomodachi.berkeleybop.org/static
AMIGO_TERM_REGEXP:
comment: The regular expressions to identify internal ontology ids.
type: string
value: 'all|GO:[0-9]{7}'
AMIGO_VERBOSE:
comment: Log verbose AmiGO debugging messages.
type: boolean
value: 0
AMIGO_WORKING_PATH:
comment: Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.
type: directory
value: /tmp
GOLR_CATALOG_LOCATION:
comment: The location of the GO catalog file for various work.
type: file
value: '/home/bbop/local/src/svn/geneontology.org/trunk/ontology/extensions/catalog-v001.xml'
GOLR_GAF_LIST:
comment: The list of GAFs to load.
type: list
value:
- http://www.geneontology.org/gene-associations/submission/paint/pre-submission/gene_association.paint_other.gaf
- http://www.geneontology.org/gene-associations/gene_association.GeneDB_Lmajor.gz
- http://www.geneontology.org/gene-associations/gene_association.GeneDB_Pfalciparum.gz
- http://www.geneontology.org/gene-associations/gene_association.GeneDB_Tbrucei.gz
- http://www.geneontology.org/gene-associations/gene_association.PAMGO_Atumefaciens.gz
- http://www.geneontology.org/gene-associations/gene_association.PAMGO_Ddadantii.gz
- http://www.geneontology.org/gene-associations/gene_association.PAMGO_Mgrisea.gz
- http://www.geneontology.org/gene-associations/gene_association.PAMGO_Oomycetes.gz
- http://www.geneontology.org/gene-associations/gene_association.aspgd.gz
- http://www.geneontology.org/gene-associations/gene_association.cgd.gz
- http://www.geneontology.org/gene-associations/gene_association.dictyBase.gz
- http://www.geneontology.org/gene-associations/gene_association.ecocyc.gz
- http://www.geneontology.org/gene-associations/gene_association.fb.gz
- http://www.geneontology.org/gene-associations/goa_chicken.gaf.gz
- http://www.geneontology.org/gene-associations/goa_chicken_complex.gaf.gz
- http://www.geneontology.org/gene-associations/goa_chicken_rna.gaf.gz
- http://www.geneontology.org/gene-associations/goa_cow.gaf.gz
- http://www.geneontology.org/gene-associations/goa_cow_complex.gaf.gz
- http://www.geneontology.org/gene-associations/goa_cow_rna.gaf.gz
- http://www.geneontology.org/gene-associations/goa_dog.gaf.gz
- http://www.geneontology.org/gene-associations/goa_dog_complex.gaf.gz
- http://www.geneontology.org/gene-associations/goa_dog_rna.gaf.gz
- http://www.geneontology.org/gene-associations/goa_human.gaf.gz
- http://www.geneontology.org/gene-associations/goa_human_complex.gaf.gz
- http://www.geneontology.org/gene-associations/goa_human_rna.gaf.gz
- http://www.geneontology.org/gene-associations/goa_pig.gaf.gz
- http://www.geneontology.org/gene-associations/goa_pig_complex.gaf.gz
- http://www.geneontology.org/gene-associations/goa_pig_rna.gaf.gz
- http://www.geneontology.org/gene-associations/goa_uniprot_all_noiea.gaf.gz
- http://www.geneontology.org/gene-associations/gene_association.gramene_oryza.gz
- http://www.geneontology.org/gene-associations/gene_association.jcvi.gz
- http://www.geneontology.org/gene-associations/gene_association.mgi.gz
- http://www.geneontology.org/gene-associations/gene_association.pombase.gz
- http://www.geneontology.org/gene-associations/gene_association.pseudocap.gz
- http://www.geneontology.org/gene-associations/gene_association.rgd.gz
- http://www.geneontology.org/gene-associations/gene_association.sgd.gz
- http://www.geneontology.org/gene-associations/gene_association.sgn.gz
- http://www.geneontology.org/gene-associations/gene_association.tair.gz
- http://www.geneontology.org/gene-associations/gene_association.wb.gz
- http://www.geneontology.org/gene-associations/gene_association.zfin.gz
GOLR_METADATA_LIST:
comment: 'The full path to the YAML config files directory. In that directory, all files like *config.yaml will be scanned for use.'
type: list
value:
- '~/local/src/git/amigo/metadata/ont-config.yaml'
- '~/local/src/git/amigo/metadata/bio-config.yaml'
- '~/local/src/git/amigo/metadata/bio-config.browse.yaml'
- '~/local/src/git/amigo/metadata/ann-config.yaml'
- '~/local/src/git/amigo/metadata/ann-config.browse.yaml'
- '~/local/src/git/amigo/metadata/general-config.yaml'
- '~/local/src/git/amigo/metadata/model-ann-config.yaml'
- '~/local/src/git/amigo/metadata/noctua-model-meta-config.yaml'
- '~/local/src/git/amigo/metadata/protein-family-config.yaml'
- '~/local/src/git/amigo/metadata/ann_ev_agg-config.yaml'
GOLR_METADATA_ONTOLOGY_LOCATION:
comment: The full path to the ontology YAML config file. This is core for any ontology-related load.
type: file
value: '/home/bbop/local/src/git/amigo/metadata/ont-config.yaml'
GOLR_NOCTUA_ENRICHED_MODEL_PATH:
comment: The list of ontologies to load.
type: directory
value: '/home/bbop/local/src/git/noctua-models/models/'
GOLR_ONTOLOGY_LIST:
comment: The list of ontologies to load.
type: list
value:
- http://purl.obolibrary.org/obo/go/extensions/go-gaf.owl
- http://purl.obolibrary.org/obo/eco.owl
- http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl
- http://purl.obolibrary.org/obo/cl/cl-basic.owl
- http://purl.obolibrary.org/obo/go/extensions/gorel.owl
- http://purl.obolibrary.org/obo/pato.owl
- http://purl.obolibrary.org/obo/po.owl
- http://purl.obolibrary.org/obo/chebi.owl
- http://purl.obolibrary.org/obo/uberon/basic.owl
- http://purl.obolibrary.org/obo/wbbt.owl
- http://purl.obolibrary.org/obo/go/extensions/go-modules-annotations.owl
- http://purl.obolibrary.org/obo/go/extensions/go-taxon-subsets.owl
GOLR_PANTHER_FILE_PATH:
comment: The location of the cleaned PANTHER file for the proper loading into GOlr.
type: directory
value: '/home/bbop/local/src/svn/geneontology.org/trunk/experimental/trees/panther_data/'
OWLTOOLS_MAX_MEMORY:
comment: The maximum amount of memory to give OWLTools processes.
type: string
value: 192G
OWLTOOLS_USE_MERGE_IMPORT:
comment: Whether or not to include --merge-import http://purl.obolibrary.org/obo/go/extensions/go-gaf.owl.
type: boolean
value: 1
OWLTOOLS_USE_REMOVE_DISJOINTS:
comment: Whether or not to include --remove-disjoints.
type: boolean
value: 1