Tool access

Signing up for your AWS account

1. Go to http://aws.amazon.com, and then click Sign Up.
2. Follow the on-screen instructions.
3. Additional information on getting started with AWS can be found at http://aws.amazon.com/getting-started/

Note: Part of the sign-up procedure involves receiving a phone call and entering a PIN using the phone keypad.

Creating your AWS Key Pair

1. Open the Amazon EC2 console.
2. From the navigation bar, select US East (N. Virginia) Region for the key pair.
3. Click Key Pairs in the navigation pane.
4. Enter a name for the new key pair in the Key pair name field of the Create Key Pair dialog box, and then click Create.
5. The private key file is automatically downloaded by your browser. The base file name is the name you specified as the name of your key pair, and the file name extension is .pem. Save the private key file in a safe place. (ie. ~/.ssh/my-key-pair.pem)

Mac and Linux

• If you are on a Mac or Linux system and do not have a .ssh directory, run the command below from a terminal.

mkdir ~/.ssh/

• Now move your private key to the .ssh directory.

mv ~/Downloads/<my-key-pair.pem> ~/.ssh

• Set the correct permissions.

chmod 600 ~/.ssh/<my-key-pair.pem>

Windows

• If you are on a Windows system, please follow the instructions on converting your pem key to a ppk using PuTTygen

Launch Server from Amazon Machine Image (AMI)

1. From the AWS console navigate to Services --> EC2 and click on Launch Instance
2. You should now be in the Choose AMI menu. Click on Community AMIs and search for PLACEHOLDER click Select
3. Select a size for the instance

Accessing the Shared Hackathon Server

Mac and Linux

1. If you are using a Mac of Linux machine you can simply open a terminal and ssh to the box using the private key that was provided to you.

ssh -i <path-to-private-key> <username>@dashnode.b12x.org

Windows

Install and Generate .ppk File

1. Download and install PuTTY from the Putty download page. Be sure to install the entire suite.
2. Start PuTTYgen (for example, from the Start menu, click All Programs > PuTTY > PuTTYgen).
3. Under Type of key to generate, select SSH-2 RSA.
4. Click Load. By default, PuTTYgen displays only files with the extension .ppk. To locate your .pem file, select the option to display files of all types.
5. Click Save private key to save the key in the format that PuTTY can use. PuTTYgen displays a warning about saving the key without a passphrase. Click Yes.
6. Specify the same name for the key that you used for the key pair (for example, my-key-pair). PuTTY automatically adds the .ppk file extension.

Note: Your private key is now in the correct format for use with PuTTY. You can now connect to your instance using PuTTY's SSH client.

Launch Putty and Connect to Server

1. Start PuTTY (from the Start menu, click All Programs > PuTTY > PuTTY).
2. In the Category pane, select Session and complete the following fields:
3. In the Host Name box, enter <username>@dashnode.b12x.org Note: if you are connecting to a server you created from the public AIM, please enter the following into the Host Name box <ubuntu>@<your-public-ip-address>
4. Under Connection type, select SSH.
5. Ensure that Port is 22.
6. In the Category pane, expand Connection, expand SSH, and then select Auth. Complete the following:
7. Click Browse.
8. Select the .ppk file that you generated for your key pair, and then click Open.
9. (Optional) If you plan to start this session again later, you can save the session information for future use.
10. Select Session in the Category tree, enter a name for the session in Saved Sessions, and then click Save.
11. Click Open to start the PuTTY session.
12. If this is the first time you have connected to this instance, PuTTY displays a security alert dialog box that asks whether you trust the host you are connecting to. Click Yes.

Access to the tools during hackathon

to be completed...

• The IT infrastructure necessary to develop and test code quickly (hack without looking back)

The following items will be documented very shortly
(Note that order may change:)

• Using the NMDP-developed AMI
• Installing the software on your own system
• finding the data on the AMI
• logging into the NMDP-provided instance
• requesting an account on the NMDP-provided instance
• tools included on the AMI, and NMDP-provided instance

Tools included on the AMI (and on the NMDP-provided instance)

• standard Linux system tools, including wget, curl, emacs, vim
• source control manipulation tools: git, subversion
• java development tools: openjdk 1.7, maven
• pipeline related tools: nmdp-ngs-tools, SSAKE, bwa, samtools, gl-tools, blat, sra-toolkit
• misc tools: groovy