Creating an AMI on EC2

Notes About Creating a New EC2 AMI

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The following are notes taken when creating the Amazon Machine Instance used for the CSG pipeline process. These notes assume you have already created an EC2 account and have the certificates and keys set up properly.

Launch an instance

 Login to https://console.aws.amazon.com/ec2

Pay attention to the region you are using, at least for now it seems any StarCluster activity must be in us-east-1. Launch a new instance which we will use to set up the software and ultimately save it as an AMI.

 EC2 DashBoard -> Launch Instance
 Class Wizard
 Ubuntu Server 12.04.1 LTS   64 bit
 Instance type -> Micro,  EC2, no preference        # Memory size does not matter
 Advanced Instance Options  (take defaults)
 Storage Device Configuration -> Edit
 Change volume to 30G -> Save -> Continue           # Storage size does not matter
 Key Name = CSG 8G biopipe; ubuntu 12.04
 Create Key/Pair if you need to, Name the PEM and save the pem file for access by ssh
 Choose a Security Group  (take default)
 Launch
   No need to Create Status Check Alarms
   No need to Create EBS Volumes

Install the pipeline software

In a terminal on your workstation, copy the

ssh -i ~/.ssh/AWS/CSG.pem ubuntu@ec2-23-20-32-7.compute-1.amazonaws.com mkdir debs scp dev/biopipe/*.deb dev/umake/*.deb root8g:debs

ssh -i ~/.ssh/AWS/CSG.pem ubuntu@ec2-23-20-32-7.compute-1.amazonaws.com

sudo dpkg -i debs/biopipe-align_0.6_amd64.deb Selecting previously unselected package biopipe-align. (Reading database ... 25372 files and directories currently installed.) Unpacking biopipe-align (from .../biopipe-align_0.6_amd64.deb) ... Setting up biopipe-align (0.6) ... Created symlink '/usr/local/bin/gen_biopipeline.pl' to make running the aligner easier.

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2. 'java' is not installed, do 'sudo apt-get install java-common default-jre'
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5. 'make' is not installed, do 'sudo apt-get install make'
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8. 'libssl0.9.8' is not installed, do 'sudo apt-get install libssl0.9.8'
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11. '/usr/local/biopipe/test/align' does not exist so you cannot test this install
12. Install it by doing 'sudo dpkg -i biopipe-test_*.deb'
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etc

If there were messages about missing packages, install them now

 sudo apt-get install make libssl0.9.8 java-common default-jre

sudo dpkg -i debs/biopipe-testalign_0.6_amd64.deb

/usr/local/biopipe/bin/gen_biopipeline.pl --test ~/testalign

Create Image

 Image Name   csg-biopipe_instance
 Image Description:  Image for CSG Biopipe instance
 Volume Size:  30GB
 Take defaults otherwise

See notice about

 View pending image ami-d27ec7bb

AMI: Ubuntu Cloud Guest AMI ID ami-3d4ff254 (x86_64) Name: Ubuntu Server 12.04.1 LTS Description: Ubuntu Server 12.04.1 LTS with support available from Canonical (http://www.ubuntu.com/cloud/services). Edit AMI Number of Instances: 1 Availability Zone: No Preference Instance Type: Micro (t1.micro) Instance Class: On Demand Edit Instance Details EBS-Optimized: No Monitoring: Disabled Termination Protection: Disabled Tenancy: Default Kernel ID: Use Default Shutdown Behavior: Stop RAM Disk ID: Use Default Network Interfaces: Secondary IP Addresses: User Data: IAM Role: Edit Advanced Details Key Pair Name: CSG Edit Key Pair Security Group(s): sg-a098e9c8 Edit Firewall

Launch an AMI EC2 DashBoard -> AMIs -> Select CSG instance -> Launch Instance Launch Instances (take defaults) Advanced Instance Options (take defaults) Storage Device Configuration -> Edit Change volume to 30G or whatever -> Continue Instance Details

 Key Name = test of instance

Create Key/Pair if you need to, Name the PEM (e.g. CSG) and save the CSG.pem file

Choose a Security Group (take dfeault)

 sg-a098e9c8 - quick-start-1

Review -> Launch