RNA-seq Bioinformatics

Introduction to bioinformatics for RNA sequence analysis

Log into AWS

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

Basic intro to the instance (top, resources available, mount location of volumes, etc.).

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 (not recommended unless you are already familiar with and using AWS) OR you will need to be assigned an AWS account using the IAMS system. If neither of these is possible, the instructors will have to launch an instance for you and provide the login details.

Logging in with ssh (Mac/Linux)

chmod 400 CBWNY.pem
ssh -Y -i CBWNY.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.

Copying files to your computer

scp -i CBWNY.pem ubuntu@[your dns name]: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 two directories: “tools” and “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 CBWNY.pem __MY_DATA__ ubuntu@__YOUR_DNS_NAME__:/