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How to create bedbase config file

Bedbase config file is yaml file with 4 parts:

  • paths and vector models
  • relational database credentials
  • qdrant credentials
  • server information
  • remote info
  • pephub info
  • s3 credentials

Example:

path:
  remote_url_base: http://data.bedbase.org/
  region2vec: databio/r2v-encode-hg38
  vec2vec: databio/v2v-geo-hg38
  text2vec: sentence-transformers/all-MiniLM-L6-v2
database:
  host: $POSTGRES_HOST
  port: 5432
  password: $POSTGRES_PASSWORD
  user: $POSTGRES_USER
  database: bedbase2
qdrant:
  host: $QDRANT_HOST
  port: 6333
  api_key: $QDRANT_API_KEY
  collection: bedbase2
server:
  host: 0.0.0.0
  port: 8000
s3:
  endpoint_url: $AWS_ENDPOINT_URL
  aws_access_key_id: $AWS_ACCESS_KEY_ID
  aws_secret_access_key: $AWS_SECRET_ACCESS_KEY
  bucket: bedbase
phc:
  namespace: databio
  name: bedbase_all
  tag: default
access_methods:
  http:
    type: "https"
    description: HTTP compatible path
    prefix: https://data2.bedbase.org/
  s3:
    type: "s3"
    description: S3 compatible path
    prefix: s3://data2.bedbase.org/
  local:
    type: "https"
    description: How to serve local files.
    prefix: /static/