Galaxy Tool Management

Overview

question Questions

• How to install, update, and maintain Galaxy tools?
• How to extract a list of tools from a workflow or Galaxy instance?

objectives Objectives

• Learn about Ephemeris
• Extract a list of tools from a workflow
• Install these tools into a given Galaxy

time Time estimation: 45 minutes

Overview

This tutorial will introduce you to one of Galaxy’s associated projects - Ephemeris. Ephemeris is a small Python library and set of scripts for managing the bootstrapping of Galaxy plugins - tools, index data, and workflows. It aims to help automate, and limit the quantity of manual actions admins must do in order to maintain a Galaxy instance.

Agenda

1. Background
2. Requirements
3. Extracting Tools
4. Installing Tools
5. Tool Testing
6. Obtaining a Tool List
7. Production Best Practices

Background

You are an administrator of your lab’s Galaxy. A colleague has approached you with a request to run a specific Galaxy workflow on the lab’s data. In order to run this workflow you have to accomplish several substeps first. You will need to:

• identify what tools are required for the workflow
• and install these on your Galaxy instance

Requirements

To run this tutorial, first you will need to install Ephemeris. We recommend installing it in a virtualenv.

Extracting Tools

Galaxy workflow files are complex json documents, and the process of mapping the tool IDs to a ToolShed repository and revision is not trivial. Workflow files contain tool IDs which look like:

toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1
toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1

However in order to actually install these tools, we need to convert the ID into a revision number. Ephemeris takes care of this process for us, and identifies the exact revision which corresponds to the version listed in your workflow. For example, FastQC version 0.71 corresponds to revision ff9530579d1f in the ToolShed.

- name: fastqc
  owner: devteam
  revisions:
  - ff9530579d1f
  tool_panel_section_label: Tools from workflows
  tool_shed_url: https://toolshed.g2.bx.psu.edu

Let’s try running this on a real worfklow.

hands_on Hands-on: Extracting a list of tools from a workflow

1. Download the mapping workflow:

   $ wget https://galaxyproject.github.io//training-material/topics/sequence-analysis/tutorials/mapping/workflows/mapping.ga
   

2. Use the Ephemeris command workflow-to-tools to extract the tool list from this workflow, into a file named workflow_tools.yml.

   question Question

   What did your command look like?

   solution Solution

   $ workflow-to-tools -w mapping.ga -o workflow_tools.yml -l "mapping tools"
   

3. Inspect the tool list file.

Installing Tools

Now that you have extracted a list of tools, let’s install these to Galaxy. In order to accomplish this section you will need:

• The URL of your Galaxy instance
• To be an admin of this Galaxy
• The API key for your account

There are additionally two ways to install tools, we’ll show both:

hands_on Hands-on: Installing tools from a specific tool name

1. Use the Ephemeris command shed-tools to install the tool bwa, owned by user devteam into a section named Mapping

   question Question

   What did your command look like?

   solution Solution

   Note that your API key and URL will probably be different than in the example command below:

   $ shed-tools install -g https://your-galaxy -a <api-key> --name bwa --owner devteam --section_label Mapping
   

This provides an easy way to do one-off installation of tools, but is less convenient if you want to install many tools. For that, you can install from a yaml file:

hands_on Hands-on: Installing tools from a tool list

1. (optional) Use the tail command to watch the installation proceed

2. Use the Ephemeris command shed-tools to install all of the tools from the workflow_tools.yml file to your Galaxy.

   question Question

   What did your command look like?

   solution Solution

   Note that your API key and URL will probably be different than in the example command below:

   $ shed-tools install -t workflow_tools.yml -g "http://127.0.0.1:8080" -a "5cfd0d5f88c8addd5700b6a522a6a983"
   

3. Open your Galaxy’s admin interface and check that the tools have been installed.

4. Using the UI import the workflow file that you used, mapping.ga.

Occasionally this will fail due to network issues, if it does just re-run the shed-tools installation process until it succeeds. This is a known issue the developers are working on.

Tool Testing

Having the tools installed is a good first step, but usually your users will expect that they actually work as well. You can use Ephemeris to automatically test all of the installed tools

hands_on Hands-on: Test the installed tools

1. Use the Ephemeris command shed-tools to test all of the tools from the workflow_tools.yml file on your Galaxy.

   question Question

   What did your command look like?

   solution Solution

   Note that your API key and URL will probably be different than in the example command below:

   $ shed-tools install -t workflow_tools.yml -g "http://127.0.0.1:8080" -a "5cfd0d5f88c8addd5700b6a522a6a983" --test
   

This can give you some more confidence that things are working correctly. Oftentimes, users provide workflows for biological domains that we are not familiar with, so knowing how we can test these tools is impossible for us as admins. Leveraging the built-in tool test cases can give you reassurance that things are functional before you inform your users of the new tools.

Obtaining a Tool List

Sometimes your users might request that you install all of the same tools as they were previously using in a domain specific server. Ephemeris offers functionality to obtain a tool_list.yaml for all of the tools installed on an instance.

hands_on Hands-on: Obtain UseGalaxy.eu’s tool list

1. Use the Ephemeris command get-tool-list to obtain the full set of tools installed to UseGalaxy.eu

   question Question

   What did your command look like?

   solution Solution

   This command does not require authentication and can be used to obtain the tool list from any public Galaxy server:

   $ get-tool-list -g "https://usegalaxy.eu" -o "eu_tool_list.yaml"
   

We will not install the tools from that server as the EU Galaxy server has more tools than most other known Galaxies, but it is useful as an example of how you can use Ephemeris to help you mirror another Galaxy instance to meet user needs.

Production Best Practices

Servers in usegalaxy.\* network use Ephemeris extensively to manage their large tool sets.

UseGalaxy.eu and UseGalaxy.org.au have different approaches:

• AU maintains separate yaml files per toolbox category, which allows easily identifying where tools should be added or found to add new revisions. They follow a cycle of adding the tool to their yaml file, triggering installation, and then updating the yaml files from the current server status.
• EU maintains yaml files roughly per domain, it is not as clear of an ordering. They maintain a yaml file where humans add the tools which should be installed in a given category, and lock files are automatically generated from these with the latest revision if it is missing. They follow a cycle of updating the lock files with the latest available revisions of tools, and then installing from these lock files any missing revisions. They use a Jenkins server to automatically run tool installation weekly.

If running ephemeris at the command line is not your preference, there is also an Ansible role and a sample playbook that can help automate some tasks.

keypoints Key points

• Ephemeris and automation help with the tool management on Galaxy
• There are tool management best practices you can learn from
• Do not manage your Galaxy's tools manually

congratulations Congratulations on successfully completing this tutorial!

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