RNA-seq Bioinformatics

Introduction to bioinformatics for RNA sequence analysis

Log into AWS

Using cloud computing to complete this course involves two major components: (1) Launching an instance on the cloud (essentially renting a virtual computer by the hour and turning it on) and (2) logging into that instance.

Covered in this section: logging into AWS EC2 console, starting an instance from the course AMI and configuring it in the console (select instance AMI, instance type, instance details, storage volumes, tags, security group, and key pairs).

Launching an AWS instance for the course

In the previous section Introduction to AWS we reviewed fundamental concepts of cloud computing and some of the jargon and features specific to AWS. In this section we will learn how to launch an instance specifically for this course.

In order to launch your own instance you will either need to use your own personal AWS account, an account provided through your institution OR if you are taking a live version of this course you will be assigned an AWS account using the IAMS system. The following instructions are used for a live version of this course, but the process would be essentially the same when using a personal or institutional account.

Briefly the process for launching an EC2 instance for this course involves these steps:

  1. Login to AWS using the specific url and credentials (user/password) you were provided.
  2. Search for and select EC2 to access the EC2 console.
  3. Select Launch Instance, search for “cshl-seqtech-2020” in Community AMIs and Select.
  4. Choose “m5.2xlarge” instance type.
  5. Select one instance to launch, and select “Protect against accidental termination”.
  6. Make sure that you see two snapshots.
  7. Create a tag with name=StudentName (We recommend First initial and last name. e.g. MGriffith).
  8. Choose existing security group called “SSH and HTTP”. Review and Launch.
  9. Choose an existing key pair (cshl_2020_student).
  10. View instances and wait for your instance to finish initiating.
  11. Find your instance in console and select it, then hit connect to get your public.ip.address.
  12. Login to the instance as described below.

Logging in to your own EC2 instance


Logging in with Terminal (Mac/Linux)

chmod 400 cshl_2020_student.pem
ssh -i cshl_2020_student.pem ubuntu@[your ip address]

-i selects a file from which the public key authentication is read. ubuntu is the name of a user on the system you are logging into (a default user of the Ubuntu operating system). [your ip address] is the address of the linux system on Amazon that you are logging into. Instead of ip address you can also use a public dns name.

Logging in with PuTTy (Windows)

To configure PuTTy, start PuTTy and do the following:

Logging in with putty (Windows)

Logging in with putty (Windows)

Logging in with putty (Windows)

Logging in with putty (Windows)

Copying files to your computer

scp -i cshl_2020_student.pem ubuntu@[your ip address]:nice_alignments.bam .

http://[your ip address]/ or http://[your dns name]

File system layout

When you log in, you will notice that you have one directory already: “workspace”.

Uploading your data to the AWS instance

If you would like to upload your data to the AWS instance, use the example scp command below. Be sure to replace the variables below with the local path to your data, MY_DATA, and the amazon instance IP, YOUR_IP_ADDRESS.

scp -i cshl_2020_student.pem __MY_DATA__ ubuntu@[your ip address]:/

Doing this course outside of a workshop

If you are trying to do this course on your own using the online materials only, of course an AWS EC2 instance has not been set up for you. If you have access to an AWS account though you can can start with the same Amazon AMI we use to create instances for each student. Currently this is:

Name: cshl-seqtech-2020 (ID: ami-09ecbedc3b79937e3) available in the US East, N. Virginia region (us-east-1).

We typically use an instance type of m5.2xlarge. For detailed instructions on how we created the AMI and configure each instance, please refer to the AWS Setup page.

Basic introduction to your EC2 instance

Once you are logged into your EC2 instance using ssh, the following commands can be used to explore basic information about the machine

#How are storage volumes mounted?

#How much storage space in being used for various mount points?
df -h

#Detailed description of hardware

#See active resource usage right now with "top".  Use "1" to see all CPUs individually.  Use "q" to exit