SNVPhyl Command-line Interface

A command-line interface to the SNVPhyl pipeline is provided by the SNVPhyl Galaxy CLI project. This automates the process of uploading data to Galaxy, setting parameters, running a workflow, and compiling results.

Installation

The SNVPhyl CLI requires Python along with some dependency modules to be installed. To install these please run:

git clone -b master https://github.com/phac-nml/snvphyl-galaxy-cli.git
pip install -r snvphyl-galaxy-cli/requirements.txt

Usage

The SNVPhyl CLI can be run using two separate methods. The first connects to an existing Galaxy instance and executes the SNVPhyl pipeline. The second method will start a Galaxy instance using Docker, and then run the SNVPhyl pipeline, cleaning up the Docker instance after completion. For example input data please see the provided example-data/ directory.

Galaxy

To execute SNVPhyl within an existing Galaxy installation, please run:

bin/snvphyl.py --galaxy-url http://galaxy --galaxy-api-key 1234 --fastq-dir example-data/fastqs/ --reference-file example-data/reference.fasta --output-dir output

This assumes your Galaxy instance has all the SNVPhyl dependency tools and workflows pre-installed. If this is not the case, an alternative is to use the Docker method.

Docker

Assuming you have Docker installed and configured to run without sudo, then the SNVPhyl pipeline can be run without an existing Galaxy installation with:

bin/snvphyl.py --deploy-docker --fastq-dir example-data/fastqs/ --reference-file example-data/reference.fasta --output-dir output1

Please see the SNVPhyl Galaxy CLI project for additional details.