Private Registries

Overview

BioContext7 can connect to private tool registries in addition to the public bio.tools index. This is useful for institutional tools, proprietary pipelines, or tools under development.

Configure a Private Registry

Add a private registry to ~/.biocontext7/config.yaml:

registries:
  - name: my-institution
    type: biotools
    url: https://tools.my-institution.org/api
    auth:
      type: api_key
      key_env: MY_REGISTRY_API_KEY
  - name: internal-tools
    type: manifest
    path: /shared/biotools/manifests/

Registry Types

bio.tools Compatible

Connect to any bio.tools API-compatible registry:

registries:
  - name: elixir-be
    type: biotools
    url: https://bio.tools/api
    filters:
      collection: "ELIXIR-BE"

Manifest Directory

Point to a directory of biocontext7.json manifest files:

registries:
  - name: lab-tools
    type: manifest
    path: /lab/shared/tools/

Git Repository

Pull tool manifests from a Git repository:

registries:
  - name: team-tools
    type: git
    url: https://github.com/my-org/tool-registry.git
    branch: main
    path: manifests/

Authentication

API Key

auth:
  type: api_key
  key_env: MY_REGISTRY_API_KEY  # reads from environment variable

OAuth Token

auth:
  type: oauth
  provider: github  # uses stored OAuth token

Basic Auth

auth:
  type: basic
  username_env: REGISTRY_USER
  password_env: REGISTRY_PASS

Registry Priority

When multiple registries contain the same tool, BioContext7 uses this priority order:

Local manifests (registered via bc7 register)
Private registries (in config order)
nf-core modules
bio.tools public index

Sync Private Registries

# Sync all registries
bc7 sync all
 
# Sync a specific registry
bc7 sync my-institution
 
# Check sync status
bc7 sync status

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