Amazon_Cloud.md

Amazon Cloud

 

1. Tutorial: Getting started with Amazon EC2 Linux instances

Step-by-step:
     Step 1: Prerequisites
     Step 2: Launch an instance
     Step 3: Connect to your instance
     Step 4: Clean up your instance

2. Choose the cfCloud Amazon Machine Image (AMI)

Tutorail: AWS EC2: Create EC2 Instance (Linux)

     2.1. On the Choose an Amazon Machine Image (AMI) page, search for cfCloud AMI.

     2.2. Check the Root device type listed for each AMI. Notice which AMIs are the type that you need,
     either ebs (backed by Amazon EBS) or instance-store (backed by instance store).

     2.3. Check the Virtualization type listed for each AMI. Notice which AMIs are the type that you need,
     either hvm or paravirtual.

     2.4. Choose an AMI that meets your needs, and then choose Select.

3. Connect (login) to AMI and activate cfCloud environment

Tutorial: AWS EC2: Connect to Linux Instance using SSH

# Example SSH:
ssh -i "cf_Cloud.pem" [email protected]

conda info --envs
conda activate cfcloud

4. Download resources

• Bowtie2 Reference Genome
  Can be downloaded from Illumina iGenomes

# e.g. hg19:
cd ~/cfCloud/resources
wget http://igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz
tar -xzf Homo_sapiens_UCSC_hg19.tar.gz