Overview

SNVPhyl can be directly installed within an existing Galaxy instance. There are a few necessary steps that must take place for installing to a local Galaxy:

  1. Installing Build Dependencies
  2. Installing the SNVPhyl dependency tools.
  3. Importing the SNVPhyl Galaxy workflows.

Installing Build Dependencies

Installing Galaxy tools involves building many packages from source. Please make sure you have the standard build tools and development packages installed on the Galaxy system before proceeding. In particular, please make sure that Perl, Python, Java, Git, Mercurial, GCC/G++, CMake, zlib-devel, ncurses-devel, expat-devel, python-pip, python-devel, libyaml-devel, and CPANminus are all installed. The virtual machine build script located here can be used as a rough guide for any necessary dependencies for CentOS.

Installing the SNVPhyl Tools

The SNVPhyl tools are managed within a Galaxy Toolshed. In particular, within https://irida.corefacility.ca/galaxy-shed/view/nml/suite_snvphyl (the IRIDA toolshed).

You will have to enable this toolshed within Galaxy before SNVPhyl can be used. The toolshed can be enabled by adding it to the config/tool_sheds_conf.xml Galaxy configuration file. Please find this file and add the line:

<tool_shed name="IRIDA" url="https://irida.corefacility.ca/galaxy-shed"/>

Once this line is added, please restart Galaxy. If you navigate to Admin, and then from here nagivate to Tools and Tool Shed > Search Tool Shed, you should see the IRIDA toolshed show up.

irida-toolshed

Once the IRIDA toolshed is installed, you should be able to search for the suite_snvphyl repository.

suite-snvphyl-repository

Please follow through the steps to install this suite of tools, making sure to leave Handle repository dependencies? and Handle tool dependencies? checked.

snvphyl-tool-dependencies

Import SNVPhyl Galaxy workflows

The current SNVPhyl Galaxy workflows can be found at SNVPhyl 0.2 Paired-end and SNVPhyl 0.2 Paired-end invalid positions. Please import these workflow files into Galaxy by navigating to Workflow > Upload or import workflow. On completion you should have a set of workflows available.

snvphyl-import-workflows

Installation should now be complete. Please see the Usage documentation for more information on how to use SNVPhyl.