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      Bioinformatics: Command Line/R Prerequisites 2020

Home
Introduction
Intro to the Workshop and Core
Schedule
Resources
Zoom help
Slack help
Software and Links
Cheat Sheets
Intro CLI
Logging in
Introduction to the Command Line part 1
Introduction to the Command Line part 2
The cluster and modules
Introduction to Python
Python Part1, Background
Python Part2, Data Types
Python Part2, Solutions
Python Part3, Flow Control
Python Part3, Solutions
Python Part4, Working with Files
Python Part4, Solutions
Advanced CLI
Advanced Command Line
Advanced Challenge Solutions
A Simple Bioinformatics Workflow
Software Installation
Using make and cmake
Using Conda
Getting set up with AWS
AWS Event Engine
Starting and Stopping your AWS Instance
Introduction to R
Introduction to R
Introduction to tidyverse
Organizing, manipulating, and visualizing data in the tidyverse
Advanced R
Linear models in R
ETC
Closing thoughts
Github page
Biocore website

Log into Event Engine

  1. Go to https://dashboard.eventengine.run.

  2. Enter the event hash (provided at the beginning of this workshop). Then click Accept Terms and Login

  3. Select Sign In with your social account

  4. Enter your amazon.com credentials. These credentials are only used to identify you for this workshop.

  5. Once the event has started, the Team Dashboard will become available.

  6. Click on SSH Key, then Download Key. Save this key somewhere safe.

  7. Click OK to close the window and then select AWS Console from the main Dashboard.

  8. Click Open AWS Console to open the AWS Console

Launch the CloudFormation Stack

cloudformation-launch-stack

Instructions

  1. Launch the AWS CloudFormation in your AWS account using the Launch Stack button above.
  2. Click “Next”
  3. Enter Parameters for the stack.
    • For the KeyPair, select “ee-default-keypair” from the dropdown
    • For the UserList, choose a username and password, and enter them in the format “username,password”
    • For the VPCId parameter, use your Default VPC (172.31.0.0/16)
    • For the VPCSubnet parameter, choose a subnet within the Default VPC (172.31.0.0/20)
    • Leave the other defaults alone.
  4. Click Next
  5. Click Next
  6. Acknowledge that AWS CloudFormation might create IAM resources, and click Create Stack

  7. After 5 minutes, follow the link in the Outputs tab of your AWS CloudForamtion Stack to access RStudio.

  8. Accept the warning from your browser about the certificate being self-signed. This gives us encrypted, HTTPS access to RStudio without purchasing a domain name or SSL certificate.

  9. Login to RStudio using the credentials you provided to the AWS CloudFormation template.