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
Install
=======
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](https://wiki.galaxyproject.org/ToolShed) 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 https://irida.corefacility.ca/gitlab/irida/irida-install-documentation/tree/feature/galaxy-setup/galaxy.
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 @@ $ ./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**. 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.
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment