BioContext7

Team Usage

Use BioContext7 in a team or organizational setting

Overview

BioContext7 supports team-level configuration for shared registries, tool preferences, and pipeline templates.

Shared Configuration

Create a .biocontext7/config.yaml in your project root to share settings across team members:

# .biocontext7/config.yaml (committed to repo)
default_target: nextflow
prefer_nfcore: true
max_results: 20
 
registries:
  - name: team-tools
    type: manifest
    path: ./tools/
 
skills:
  - path: ./skills/

Team members inherit these settings automatically when working in the project directory.

Shared Tool Registry

Maintain a team tool registry in version control:

project/
├── .biocontext7/
│   └── config.yaml
├── tools/
│   ├── custom-aligner/
│   │   └── biocontext7.json
│   └── qc-pipeline/
│       └── biocontext7.json
└── skills/
    └── team-rnaseq.yaml

Pipeline Templates

Share pipeline templates across the team:

# skills/team-rnaseq.yaml
name: team-rnaseq
description: Standard RNA-seq pipeline for our lab
steps:
  - name: qc
    tool: fastqc
  - name: trim
    tool: trim-galore
    params:
      quality: 20
      length: 36
  - name: align
    tool: star
    params:
      genome: /shared/genomes/GRCh38
    depends_on: [trim]
  - name: count
    tool: featurecounts
    depends_on: [align]

Environment Consistency

Use BioContext7's environment export for reproducible installations:

# Export current environment
bc7 env export > bc7-environment.yaml
 
# Recreate on another machine
bc7 env create bc7-environment.yaml

The exported file captures:

  • BioContext7 version
  • Python version
  • Installed tool versions
  • Registry configuration
  • Container image digests

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