Genomics Workspace

Genomics workspace is a open-source project created by i5k workspace of NAL.

In this project, we produced a Django website with functionality of common sequence searchs including BLAST, HMMER, and Clustal.

Leveraging the admin page of Django and task queue by RabbitMQ and Celery, it’s much easier to manage the sequence databases and provide services to end-users.

All source codes of genomics workspace are in our github repo.

Note

You can try genomics workspace on our live services:

• BLAST: https://i5k.nal.usda.gov/webapp/blast/
• HMMER: https://i5k.nal.usda.gov/webapp/hmmer/
• Clustal: https://i5k.nal.usda.gov/webapp/clustal/

In fact, the live services listed above are implemented by a customized version of genomics workspace. You can check the source code of it in another github repo: NAL-genomics-workspace.

Table of Contents

• 1. Pre-requisites
• 2. Setup Guide
  • 2.1. Setup Guide (CentOS)
  • 2.2. Setup Guide (MacOS)
  • 2.3. Advanced Setup
• 3. User Guide
  • 3.1. Getting started
  • 3.2. BLAST Database Configuration
  • 3.3. HMMER Database Configuration
  • 3.4. Organism and Database deletion
• 4. How to Deploy
  • 4.1. Apache HTTP server and mod_wsgi
  • 4.2. RabbitMQ
  • 4.3. Celery and celerybeat
• 5. Trouble Shooting
• 6. About i5k Workplace at NAL

Indices and tables

• Index
• Module Index
• Search Page