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SNVPhyl Pipeline Tools

This document describes how to build and install the SNVPhyl tools within a custom toolshed. The tools are located under tools/. These can be packaged up and uploaded into a Galaxy Tool Shed and then later installed to an instance of Galaxy. The list of tools is given below:

  • phyml
  • smalt_collection
  • freebayes
  • core-pipeline tools

These can be installed to a Galaxy Tool Shed and then to Galaxy using the following steps.

Step 1: Building Tool Shed Packages

In order to build packages that can be uploaded to a Galaxy Tool Shed please run the following command.

./scripts/build_for_toolshed.sh

This will build a number of .tar.gz files within the build/ directory that can then be uploaded into a Galaxy Tool Shed.

Step 2: Creating Repositories for Tool Shed Packages

In order to install tools into your own local instance of a Galaxy Tool Shed, you first need to create empty repositories. This can be accomplished by:

  1. Log into your Galaxy Tool Shed. On the left panel please find and click on the Create new repository link.
  2. Fill out the name of the repository, for example for core_phylogenomics_pipeline.tar.gz you can fill out core_phylogenomics_pipeline (please make sure to name the repository the same name as the tarball minus .tar.gz). Fill out any other information.
  3. Click on Save.
  4. Repeat for any other files under build/.

Step 3: Upload Tool Shed Packages

  1. Find and click on one of your new empty repositories.
  2. In the upper right click on Upload files to repostory.
  3. From here Browse to one of the tool shed packages under build/ and upload this package.
  4. In the upper right corner under Repository Actions click on Reset all repository metadata. You should now see a screen listing the tools and dependencies of this repository.

Step 4: Install Packages to Galaxy

Once you have uploaded the packages to a Galaxy Tool Shed, you can install to a local version of Galaxy linked up to the Tool Shed by following the below steps.

  1. Go to Admin and from here in the left panel find Search and browse tool sheds.
  2. Find the Tool Shed where the tool is installed and click on Browse valid repositories. From here find the particular tool you installed.
  3. Click on the arrow next to the tool and click on Preview and install.
  4. Wait for Galaxy to install your tool.