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.

```bash
./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.

[Core Phylogenomis Pipeline]: https://github.com/apetkau/core-phylogenomics
[Galaxy Tool Shed]: https://wiki.galaxyproject.org/ToolShed
[Production Server Setup]: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
[Testing Installed Tools]: https://wiki.galaxyproject.org/TestingInstalledTools
[IRIDA Galaxy Setup]: https://irida.corefacility.ca/irida/irida-install-documentation/tree/master/galaxy
[Automated Tool Tests]: https://wiki.galaxyproject.org/AutomatedToolTests
[Hosting a Local Tool Shed]: https://wiki.galaxyproject.org/HostingALocalToolShed
[Install and Test Certification]: https://wiki.galaxyproject.org/InstallAndTestCertification
[Tool Testing Enhancements]: http://dev.list.galaxyproject.org/Tool-Testing-Enhancements-td4663799.html