TPP TWA:Tutorial
From SPCTools
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Contents |
Introduction
The TPP Web-launcher for Amazon Web Services (TWA) is a cloud computing web-based application for launching your own instance of TPP in the cloud. Based on Amazon Web Services, it simplifies the process of starting an Amazon Elastic Compute Cloud (EC2) instance with TPP already installed and ready to use.
About Tutorial
This tutorial is written for anyone interested in using a completely cloud based instance of the Trans-Proteomics Pipeline on Amazon Web Services. It will walk the user through the steps of setting up a Amazon Web Services account and then using TWA to launch a compute node on the cloud running the TPP. Users will then use TPP's Petunia web interface to submit multiple searches on AWS and view the results. Readers may find it easier to follow the tutorial if they are already familiar with the TPP's web interface and usage.
Requirements
All that is required to execute this tutorial is a Amazon Web Services account, a Internet connection, and a current version of either the Firefox or Internet Explorer web browser. Older browser versions or vendors of browsers may not support all functionality.
Tutorial
Readers should be aware that executing this tutorial will incur some AWS charges. The exact amount of these charges will vary based on a number of factors but should be on the order of $1-$4 USD.
Step 1: Starting TWA
Launch the TWA application by navigating with your web browser to http://tools.proteomecenter.org/twa. The TWA web-based application will appear as a toolbar across the top of the main page with details about the TWA application. Within this toolbar are two fields for entering a Access Key ID and the Secret Access Key, more on these in the next section. Next in the toolbar are two drop down menus, the first labeled "Tools" and the second labeled "AWS Shortcuts". The Tools submenu provides control over options along with several useful operations and is only enabled once you've successfully authenticated your access and secret keys. The AWS Shortcuts menu provides shortcut links to web forms at Amazon Web Services commonly used by TPP cloud services. The last element in the toolbar is a control button that allows you to either start or stop a EC2 instance. The button will only be enabled when successfully authenticated and its label will reflect the current state (start or stop instance).
Step 2: Creating Your Amazon Web Services Account
If you already have a Amazon Web Services account you can skip to the next step. (Please note that an AWS account is different than having an account on the normal Amazon web site). To create a new account, select "Amazon Sign In/Register" under the AWS Shortcuts menu in the TWA toolbar. A new tab should open to Amazon Web Services with details on created a new account or signing in to a existing account. Alternately you can navigate with your browser to http://aws.amazon.com/ and click on "Create a Free Account".
Step 3: Getting Your Amazon Credentials
In order for TWA to interact with Amazon Web Services on your behalf you must provide your security credentials to confirm that you are who you say you are and that you do have permissions to do what you are trying to do. These security credentials are known as an access key and is comprised of key id and secret key. This key can then be used to make secure REST or Query protocol requests to any AWS service API. And much like real life your Amazon account may have multiple access keys associated it.
All AWS accounts have what is known as root account credentials. These credentials allow full access to all resources in the account. You'll want to make sure you store your root credentials in a safe place and never share these with anyone, particularly a 3rd party AWS application as they are the "keys to the kingdom". Instead AWS provides a web service known as Identity and Access Management (IAM), which allows you to create user credentials for day-to-day interactions with AWS. Its strongly recommended that you only use these user access keys when using TWA.
You create and manage user access keys using the IAM console at Amazon Web Services. Under AWS shortcuts in the TWA toolbar there is a menu item that when selected will open a new tab/window to the console. Alternatively you can access the console at https://console.aws.amazon.com/iam/home.
Now go ahead and create a new user by selecting on users in the left side menu and then clicking on "Create New User". Name the user something suggestive of TWA, such as "TPP-TWA". Make sure you leave the "Create Access Key" checked. Click "ok" to create the user. A window should appear asking you to download your access and secret key. You can either choose to view your keys or download them to your desktop. If you don't save these keys you will have to delete and regenerate them again the next time you need them.
Next you'll have to grant permissions to the "TPP-TWA" user to enable the keys to work. Select on the user you just created and click permissions and then "Attach User Policy". The window should display a list of policy templates and allow you to create your own policies. The easiest approach is to just select "Power User Access" and select apply. This grants access to all web services to the TPP-TWA user using its access key and you are ready for the next step in the tutorial. Alternatively if you want to be a little more security minded you can scroll through the list of templates and add the following templates: Amazon EC2 Full Access, Amazon S3 Full Access, and Amazon SQS Full Access.
For more information on Amazon Web Services security credentials see:
Step 3: Signing into TWA
Using the access and secret keys from the previous step, enter them into the fields in the TWA toolbar and click on the small submission icon to sign into Amazon Web Services. Once signed in both the Tools menu and the Start Instance button should become active. If you encounter an error check that you entered your access key and secret key in correctly and try again.
Step 4: Launch a EC2 instance
Step 5: Search data with X!Tandem
Step 7: Cleanup
After you are satisfied with your results its important to cleanup your files on Amazon to avoid any additional charges as the original input data and results remain in Amazon S3 until you perform this last step. Using Petunia navigate to Account > Amazon Cloud and click on the button "Shutdown all instances and delete all data". This will ensure that any remaining instances are terminated and all data stored in Amazon S3 is removed. Note at any time you can click on this button to stop Amazon processing and remove your data.
Next Steps
For further information on using Amazon cloud services see the other tutorials and documentation on this website or post your questions to the TPP mailing list at spctools-discuss discussion group.
