Amplicon Pipeline

Run the amplicon pipeline with all tools installed inside a Docker container. Your data and the reference databases live outside the container in a directory that is "mounted" into the container at execution time. The pipeline is implemented with Common Workflow Language (CWL), allowing execution with a variety of execution platforms (see http://commonwl.org).

Requirements

• docker

To obtain docker got to https://docs.docker.com/engine/installation/

Setup and run example

1. git clone https://github.com/MG-RAST/amplicon.git

Change into cloned repository:

2. cd amplicon

Download reference databases:

3. ./setup.sh

or from within the container

docker run -v `pwd`:/amplicon -ti --rm --entrypoint bash --workdir /amplicon mgrast/amplicon:latest setup.sh

Change into the newly created Data directory:

4. cd Data

This will be your working directory. Copy or move your sequence files into this directory and rename them to R1.fastq.gz and R2.fastq.gz For example:

5. cp your_path/ your_sequence_files.R1.fastq.gz > R1.fastq.gz

6. cp your_path/ your_sequence_files.R2.fastq.gz > R2.fastq.gz

7. docker run -v `pwd`:/Data mgrast/tap:latest

Pipeline