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SNVPhyl: Whole Genome SNV Phylogenomics Pipeline

The SNVPhyl (SNV PHYLogenomics) pipeline is a pipeline for identifying Single Nucleotide Variants (SNV) within a collection of microbial genomes and constructing a phylogenetic tree. Detailed documentation can be found at http://snvphyl.readthedocs.io/. This repository contains the customized Galaxy tools for this pipeline as well as the source for the documentation.

Availability

Command-line interface

A command-line interface for SNVPhyl is available at https://github.com/phac-nml/snvphyl-galaxy-cli. This can be used to automatically prepare data and run SNVPhyl in a pre-existing Galaxy instance, or in a custom Docker container. To quickly try out SNVPhyl, the following can be run (assuming Python and Docker are installed).

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

# append `--with-docker-sudo` if docker command requires sudo
python bin/snvphyl.py --deploy-docker --fastq-dir example-data/fastqs --reference-file example-data/reference.fasta --min-coverage 5 --output-dir output1

Please see https://github.com/phac-nml/snvphyl-galaxy-cli for more details.

Nextflow

A version of SNVPhyl available for execution in Nextflow has been developed by Jill Hagey and is available at https://github.com/DHQP/SNVPhyl_Nextflow.

Galaxy

The SNVPhyl pipeline is available via a Galaxy toolshed at http://irida.corefacility.ca/galaxy-shed. Dependency tools are installable via the suite_snvphyl_x_y_z tool suite. Workflow files are available at docs/workflows/SNVPhyl/.

Please see http://snvphyl.readthedocs.io/en/latest/install/galaxy/ for more details.

Virtual Machine

A virtual machine containing the SNVPhyl workflow pipeline and Galaxy is available for download at https://sairidapublic.blob.core.windows.net/downloads/snvphyl-galaxy/snvphyl-galaxy-current.zip or, using Vagrant, can be launched like:

git clone https://github.com/phac-nml/snvphyl-galaxy.git
cd snvphyl-galaxy/vagrant
vagrant up

Galaxy and SNVPhyl can then be accessed through http://localhost:48888 with username admin@localhost.localdomain and password adminpassword.

Please see http://snvphyl.readthedocs.io/en/latest/install/virtualmachine/ for more details.

Docker

A Docker image of SNVPhyl and Galaxy can be launched by running:

docker run -d -p 48888:80 phacnml/snvphyl-galaxy-1.0.1

Galaxy and SNVPhyl can then be access through http://localhost:48888 with username admin@galaxy.org and password admin.

Please see http://snvphyl.readthedocs.io/en/latest/install/docker/ for more details, or https://github.com/bgruening/docker-galaxy-stable for details on the underlying Galaxy Docker image.

Citation

Petkau A, Mabon P, Sieffert C, Knox N, Cabral J, Iskander M, Iskander M, Weedmark K, Zaheer R, Katz L, Nadon C, Reimer A, Taboada E, Beiko R, Hsiao W, Brinkman F, Graham M, Van Domselaar G. SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology. 08/06/2017. M Gen 3(6): doi:10.1099/mgen.0.000116.

Legal

Copyright 2012-2019 Government of Canada

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this work except in compliance with the License. You may obtain a copy of the License at:

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.