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.