Centralized access to Dockerized tools and pipelines for metagenomics developed by the Human Microbiome Project members. Initially developed for the HMP Cloud Workshop, you can run common metagenomics tools on the command line interactively within Docker or run entire pipelines at once.
* 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.
The Docker site has detailed instructions for many architectures, but for some this may be as simple as:
$ sudo apt-get install docker.io [restart]
If this is the first time you've installed Docker Engine, reboot your machine (even if the docs leave this step out.)
After Docker installation, the only other dependences are python things. They can all be installed like this on Ubuntu machines. Make any changes necessary for your platform.
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 40976EAF437D05B5 sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys F76221572C52609D sudo apt-get update sudo apt install -y python3 python3-pip python-pip sudo pip3 install pyyaml requests sudo pip install pyyaml cwlref-runner
This command will create a Chiron directory:
$ git clone https://github.com/IGS/Chiron.git
How to run
There are two primary ways we intend for this to be run.
First, you can launch an interactive session for any of the tools within a Docker image. Second, we supply CWL pipelines for many tools which will allow you to run entire analysis paths at once in both a local and distributed manner. Both are described below.
Get on a cloud machine (optional)
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.
Try an interactive session
If you want to use a specific tool's docker image, you'll find scripts to run each tool such as:
This will download the Docker image if you don't already have it, then drop you to a terminal within it.
Run a pre-built analysis pipeline
Docker-enabled pipelines have been written for several analysis tools using Common Workflow Language (CWL). These are available for viewing here, and you can view help for any of the pipeline launchers named like this:
# ./Chiron/bin/strainphlan_pipeline -h
Existing tools/Docker images:
- umigs/chiron-core - Includes the HMP Client and common utilities
- umigs/chiron-phlan - Suite of -PhlAn tools, includes:
Try a Cloud session on Amazon
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:
For general instructions about launching virtual machines on AWS, Amazon has provided useful instructions here: