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:
- Installing Build Dependencies
- Installing the SNVPhyl dependency tools.
- 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.
Once the IRIDA toolshed is installed, you should be able to search for the 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.
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.
Installation should now be complete. Please see the Usage documentation for more information on how to use SNVPhyl.