Computation Examples

First-Time Setup

Sign up to AWS

1. Create an AWS Account
   • Use your sagebase.org email address for the account name
   • Enter Sage Bionetworks physical address for the address
   • You will need to use your own credit card temporarily
2. Send Mike Kellen an email to have your new AWS account added to the consolidated bill
   • Once this is done, you will no longer be billed on your own credit card
3. Log onto the AWS Console and sign up for S3, EC2, and Elastic MapReduce

Configure EC2

1. Use the AWS console to create and download an SSH key named SageKeyPair and store it in your home directory on the shared servers

Configure S3

1. Use the AWS console to make a new S3 bucket named sagetest-YourUsername and make these four subdirectories
   1. scripts
   2. input
   3. output
   4. results
   5. logs

Set up your config files for the AWS command line tools installed on the shared servers

Get your credentials

Get your security credentials from your AWS Account

• Access Key ID
• Secret Access Key

Set up s3curl

Set up your configuration files for the AWS tools installed on the shared server

1. Create the configuration file for s3curl command line tool

   ~>cat .s3curl 
   #!/bin/perl
   %awsSecretAccessKeys = (
       YourUsername => {
           id => 'YourAccessKeyID',
           key => 'YourSecretAccessKey',
       },
   );
   

2. Test that you can run s3curl

   /work/platform/bin/s3curl.pl --id $USER https://s3.amazonaws.com/sagetest-$USER/
   

Set up the Elastic MapReduce command line tools

1. Create the configuration file for the Elastic Map Reduce command line tool

   ~>cat YourUsername-credentials.json 
   {
   "access_id": "YourAccessKeyID",
   "private_key": "YourSecretAccessKey",
   "keypair": "SageKeyPair",
   "key-pair-file": "/home/$user/SageKeyPair.pem",
   "log_uri": "s3n://sagetest-YourUsername/logs/",
   "region": "us-east-1"
   }
   

2. Test it

   /work/platform/bin/elastic-mapreduce-cli/elastic-mapreduce --credentials ~/$USER-credentials.json --help