###Introduction

A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel pipeline that handles distributed execution, idempotent processing restarts and safe transactional steps. The goal is to provide a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology.

More information can be found here.

###Table of content

• I. Environment setup
  • I.1. Update the system
  • I.2. Install required packages
  • I.3. Install azure client
  • I.4. Install miniconda
  • I.5. Install additional conda packages
• II. Install bcbio-nextgen-vm
  • II.1. Add conda channel
  • II.2. Install bcbio-nextgen-vm package
• III. Setup Docker
  • III.1. Install docker
  • III.2. Setup docker groups
  • III.3. Get bcbio/bcbio docker image
  • III.4. Setup the datadir
  • III.5. Create a new docker image
  • III.6. Create and upload a docker image
  • III.7. Upgrade docker image
• IV. Setup azure environment
  • IV.1. Generate a new management certificate
  • IV.2. Uploading managementCert.cer file to Windows Azure
  • IV.3. Generate the private key
• V. bcbio cluster on Windows Azure
  • V.1. Create the elasticluster configuration file
  • V.2. Edit the elasticluster configuration file
  • V.3. Set the subscription_id

###Troubleshooting

• I. Troubleshooting - Elasticluster
  • I.1. The server encountered an internal error
  • I.2. bcbio.pickle not found
  • I.3. TypeError: expected string or buffer