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

   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 Setup CRE using the free PhenoMeNal Cloud.

2. Click “Register”

   

3. Create a user and password for your new user at the PhenoMeNal deployed CRE (at one of the partners installations).

   

4. Login to enter the PhenoMeNal deployed Galaxy instance.

   

Deployment Alternative 2: Amazon AWS

This alternative requires that you have an Amazon AWS account with credit. Please make sure to switch off the deployment once you are done using it, otherwise this will continue to use your Amazon AWS credit. Follow the directions that are available in the figures ahead to deploy a PhenoMeNal VRE to Amazon AWS. You will first select the AWS as your desired provider, then enter your AWS credentials, define an Admin user for your Galaxy instance, and finally launch the deployment process.

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

   

   Press select below the Amazon Web Services box.

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

   

   In order to secure the Galaxy instance that will be deployed within your CRE in Amazon AWS, you need to provide an email to create the account of the Galaxy administrator user, and setup the password for this user. You need to keep track of these details, as you will need them to log-in into the Galaxy instance deployed for you. With this user you will be able to administer the instance and create more users if needed.

Deployed PhenoMeNal Galaxy Instance

If you have gone through one of the two available options. The PhenoMeNal Galaxy installation consists of set of tools available through a workflow environment.

You will first need to login to the PhenoMeNal CRE deployed Galaxy instance, with the credentials that you gave in the previous steps. Go to the User drop-down menu on the top bar, as shown in Figure loginPhenoGalaxy, and select the Login option in the menu.

Find the User drop-down menu as shown, and click on the Login option to start the login. Notice that the branding can change a bit depending on where and when the instance of Galaxy was deployed. Note that 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

Enter the user and password previously used on registration.

Please note at this point that a Galaxy instance running on the PhenoMeNal sponsored CRE deployment is not meant for large scale data analysis, but for you to do some analysis within the infrastructure with data remaining in the system for a longer while than the other public instance open to the public. The PhenoMeNal sponsored CRE is not meant for sensitive or private data, so you should not upload that kind of data there. If you are not using the PhenoMeNal sponsored CRE but a deployment on your Amazon AWS account, then this does not apply of course.

Figure 8 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