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populationgenomics documentation

Setup:

  • Welcome to the CPG
  • Getting help at the CPG
  • Terminal
  • Git and GitHub
  • Hail Query and Hail Batch
  • CPG and XPG IDs
  • Python at the CPG
  • Code Editors
  • Notebooks
  • Setting up certificates from ZScaler

About the centre

  • Reproducible analyses
  • Storage policies

Libraries

  • cpg-utils
    • Configuration
    • Cloud
    • Cromwell
    • Dataproc
    • Git
    • Hail Batch
  • Production Pipelines
  • Metamist
    • Custom Cohorts

Infrastructure

  • CPG Infrastructure
  • CPG Infrastructure User Guide
  • CPG Infrastructure Developer Guide

Guides

  • Notebooks
  • Setting up a new repository
  • Style guide for R
  • Configuration
  • Data Sharing
  • Budgets
  • IGV
  • Docker Images
    • Creating Docker Images
    • Managing Images
    • Image Build Deploy
  • Kubernetes cheatsheet

Playbooks

  • Hail: Batch playbook
  • Hail: Query on Batch Playbook
  • Hail: Query on Dataproc Playbook

Python Module Index

c
 
c
- cpg_utils
    cpg_utils.cloud
    cpg_utils.config
    cpg_utils.cromwell
    cpg_utils.cromwell_model
    cpg_utils.dataproc
    cpg_utils.git
    cpg_utils.hail_batch
- cpg_workflows
    cpg_workflows.targets
    cpg_workflows.workflow

By Centre for Population Genomics

© Copyright 2024, Centre for Population Genomics.