Commit 6853c7c3 authored by Aaron Petkau's avatar Aaron Petkau

Added documentation on how to install tools

parent 5d2483d8
......@@ -8,9 +8,13 @@ Authors
Philip Mabon, Aaron Petkau
This repository contains two main sections. A set of tools under `tools/` and a workflow implementing the core phylogenomics pipeline under `workflows/`. These can be packaged up and uploaded into a [Galaxy Tool Shed]( and then later installed to an instance of Galaxy. Instructions on how to install your own local Galaxy Tool Shed and Galaxy can be found at
Building Tool Shed Packages
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.
......@@ -19,3 +23,37 @@ $ ./
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**. 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.
Step 5: Test out your tool in Galaxy
Once you've finished installing your tool, you should be able to test it out within Galaxy.
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