Centralized access to Dockerized tools and pipelines for metagenomics developed by the Human Microbiome Project members. Initially developed for the HMP Cloud Workshop.
* Pronounced KY-rən
This was initially organized for a training workshop held by the Human Microbiome Project. We want this organization of utilities to be useful for others, so an independent project was created. The name 'Chiron' was used to reflect its initial use in training. In Greek mythology Chiron was the centaur who trained greats such as Aeneas, Heracles, Jason and Achilles.
There are two primary ways we intend for this to be run. First, we will supply CWL pipelines for many tools which will allow you to run entire analysis paths at once in both a local and distributed manner. This is under development, and not yet available.
Second, you can launch an interactive session for any of the tools within a Docker image.
If you want to run things on a cloud machine, you can launch an Amazon Virtual Machine. To just run on your local machine instead, skip to the next step.
If you want to use a specific tool's docker image, you'll need to first make sure you have Docker installed, reboot, then download or clone Chiron like this:
$ git clone https://github.com/IGS/Chiron.git
Under the Chiron/bin/ directory this creates, you'll find scripts to run each tool such as:
$ ./Chiron/bin/humann2_interactive
This will download the Docker image if you don't already have it, then drop you to a terminal within it.
Docker-enabled pipelines have been written for several analysis tools using Common Workflow Language (CWL). These are available for viewing here, but work is underway to create user-friendly launchers for them. These should be available by June 15.
- umigs/chiron-core - Includes the HMP Client and common utilities
- umigs/chiron-humann2
- umigs/chiron-metacompass
- umigs/chiron-metaviz
- umigs/chiron-phlan - Suite of -PhlAn tools, includes:
- MetaPhlAn2
- GraPhlAn
- PanPhlAn
- StrainPhlAn
- umigs/chiron-qiime2
- umigs/chiron-valet
To create and configure your Amazon AWS cloud environment to execute the tools and Docker containers presented in the workshop, please use the following guide:
Cloud Workshop AWS Setup Guide
For general instructions about launching virtual machines on AWS, Amazon has provided useful instructions here:
- Discussion group site (Google groups, for collaborators)
- HMP data portal - click 'Data' to get to facet search
- HMP client - client for downloading HMP data via manifest files generated at the HMP data portal