PhenoMeNal Accessing Metabolomics Workflows in Galaxy

How to deploy PhenoMeNal CRE

1. You can create your CRE instance on a cloud provider of your choice by clicking the ‘Create Cloud Research Environment’ at the index page, or click on “Galaxy workflow” to create your workflow in a cloud environment. See figure 1 below

Figure 1 PhenoMeNal Gateway homepage is easily accessible by clicking on the 'Portal' tab in the menu on the PhenoMeNal project website. You can create workflows and browse metabolomics tools from this page.

2. Sign in to deploy the CRE via Elixir Single Sign-On (SSO) using your existing ORCID, LinkedIn or Google account credentials. Alternately sign in using your institutional account. See figure 2. For a detailed tutorial on how to register click here

Figure 2 Elixir Single Sign-On Page

3. Select your Cloud provider for the CRE deployment. You can chose to use PhenoMeNal Cloud, the free cloud service, to create your own CRE.

Deployment Alternative 1: PhenoMeNal sponsored CRE

1. Click on the “Select” button to deploy your CRE on the free PhenoMeNal cloud as shown in figure 3 below

Figure 3 Setting up of CRE using the free PhenoMeNal Cloud.

2. Click “Register” tab to access the user registration form for creating your login

Figure 4 Registration on the PhenoMeNal cloud.

3. Create a username and password as shown in figure 5.

Figure 5 User registration form

4. Login to enter the PhenoMeNal deployed Galaxy instance as shown in figure 6.

Figure 6 User login

Deployment Alternative 2: Amazon AWS

This alternative requires that you have an Amazon AWS account with credit. Follow the directions that are available in the figures ahead to deploy a PhenoMeNal VRE to Amazon AWS. Note: Please make sure to switch off the deployment once you are done using it, otherwise this will continue to use your Amazon AWS credit.

1. Click on Amazon Web services to deploy using your credentials .

Figure 7 Deployment on Amazon

2. Enter your Amazon AWS Access Key ID and Secret Access Key

Figure 8 Logging into Amazon using access key

Enter your Amazon AWS Access Key ID and Secret Access Key. If you have an account with Amazon AWS, but you don’t know how to get these access tokens, please see the following link: http://docs.aws.amazon.com/IAM/latest/UserGuide/id_credentials_access-keys.html#Using_CreateAccessKey. After that, select the region where you want to deploy.

3. Create Galaxy username and password. With this user you will be able to administer the instance and create more users if needed.

Figure 9 Creating Galaxy username and password on AWS

Deployed PhenoMeNal Galaxy Instance

The PhenoMeNal Galaxy installation consists of set of tools available through a workflow environment.

1. Login to the PhenoMeNal CRE deployed Galaxy instance using your user credentials (as acquired in the above steps). Go to the User drop-down menu on the top bar, as shown in figure 9 and select the Login option in the menu.

Figure 10 PhenoMeNal Galaxy login

Note: The branding can change a bit depending on where and when the instance of Galaxy was deployed. The Workflow and Visualization drop-down menus are disabled before login.

Presented with the login prompt, enter the email used to create your account at the CRE Portal

Figure 11 Galaxy Login: Enter your username and password

Note: The Galaxy instance running on the PhenoMeNal sponsored CRE deployment is not meant for large scale data analysis, but for some analysis within the infrastructure with data remaining in the system for a longer while than the other public instance. The PhenoMeNal sponsored CRE is not meant for sensitive or private data, so you should not upload that kind of data there. This does not apply deployment on your Amazon AWS account.

Figure 12 Galaxy CRE: After a succesful login, you should be able to upload data

Although many things work differently in the backstage of a PhenoMeNal Galaxy instance compared to other Galaxy instances, the usability and user experience is the same. As such, to familiarise yourself on how to make best use of the PhenoMeNal Galaxy CRE we can recommend the following guided Galaxy Tours: https://usegalaxy.org/tours These will give you a walkthrough the Galaxy user interface, the same used by the PhenoMeNal Galaxy CRE. After you go through those tours, you should feel comfortable to start trying the PhenoMeNal Galaxy CRE with our tools.

PhenoMeNal App Library

Browsing the PhenoMeNal App Library

The PhenoMeNal application library referred to as the “App Library” is a service catalogue providing a list of tools contained within the PhenoMeNal CRE. These tools are available via Galaxy workflows and Jupyter libraries.

To search for a metabolomics analysis tool, type the name of the tool in the search box. You can also filter your results on the basis of functionality, approach, and Instrument data type by checking the boxes of the search tree on the left

Figure 9 App Library listing the available tools

When to use Galaxy VRE: guided examples

1. This section shows you how to use Galaxy VRE. First, open the Galaxy VRE. If this is your first time in the Galaxy VRE, you need to register your account. Otherwise, please login with your registered account (Figure 12).

   

   Figure 12 Galaxy Walkthrough - Login and Register

2. The Galaxy Homepage page is divided into three columns (Figure 13). On the right hand side, you will see the history of the system. On the left hand side, you will see a various tools available. On the top, you will find the action bar that allows you to do various activities within Galaxy VRE using your own data.

   

   Figure 13 Galaxy Walkthrough - main page

3. Create a workflow using Galaxy

   a. On the top menu, select ‘Shared data’, from the dropdown menu, select ‘HIstories’.

   b. From available data set, click on ‘w4m-sacurine-statistics’ (Figure 14). It might take a while to load, please be patient.

   

   Figure 14 Galaxy Walkthrough - data loading

   The page displayed shows the public history of the data set (Figure 15). - To view each section, click on the eye symbol. - To download the data, click on hyperlink of each data set.

    **Figure 15** Galaxy Walkthrough - data loading
   
    ![figure25](./images/cre/25.png)
   
    **Figure 16** Results page for data display      
   

4. In order to analyse this data, you will need to make a copy of your data set in your own Galaxy VRE account. To this, click on the ‘Import history’ link. Click the title of the pop-up dialogue, change the title, then click on ‘Import’.

You will notice you will a list of history on the right hand side to be edited if you wish to. You can click on one of the history items and click on the visualisation button (Figure 17). You will be able to see visualisation of the data set.

Figure 17 Galaxy Walkthrough - data download