RNA-Seq analysis using Galaxy in Amazon AWS

Question: RNA-Seq analysis using Galaxy in Amazon AWS

3.2 years ago by

United States

Dear Galaxy Support:

My name is Wei-Ming Yu. I am a postdoctoral fellow from Department of Neurobiology at Harvard Medical School.

I am planing to analyze some RNA-Seq data using Galaxy in Amazon Web Service.
I followed the online document (https://wiki.galaxyproject.org/CloudMan/AWS/GettingStarted) to set up Galaxy in AWS and I have some questions regarding the setup using AWS.

Fisrt, is there a more updated instruction of how to set up AWS for Galaxy? The online one is a bit outdated as Amazon updates its AWS interface.

Second, for creating the security group, I can't change VPC to No VPC. It already assigned a default VPC-ID (vpc-2e83784a. Should I leave it as it is?

Finally, I am not sure the instance that I configured has enough resources for my project. I only signed up a Free Tier EC2 account and it only allows me to choose t1.micro as the instance type. I have 8 RNS-Seq samples (from mouse tissues) and each has thirty million pair-end reads. After unzipping the data, the fastq files are already 143GB. Would you suggest me to pay to upgrade to a better AWS service so that I won't wait indefinitely for processing my data. I am willing to pay for the better AWS service but would like your recommendation of how many resources should I obtain (instance type, vCPUs, storage)?

Thank you very much for your help! I really appreciate it.

Best,

Wei-Ming

rna-seq galaxy • 1.5k views

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modified 3.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.2 years ago by wei-ming_yu • 0

3.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Given the size of the data and current cloud configuration, the jobs will probably encounter memory issues during the latter steps of expression analysis. It may be worth it to apply for an educational (and research) grant from Amazon. These tend to process quickly if you supply them with the compute details of the experiment in the application. To get an idea about how large of an instance you should use: any resources needed by the 3rd party tools used in Galaxy will require the same resources within Galaxy as they would if used line-command.

To launch your instance, use CloudLaunch found at http://usegalaxy.org under the top masthead menu under Cloud. A "large" instance could be enough, but if you do run into a memory issue, then scaling up to an instance type with high-memory configuration would be the solution.

Thanks for using Galaxy, Jen, Galaxy team

ADD COMMENT • link modified 3.2 years ago • written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k

Update: If you would like to try the new version of Cloud Launch, you may find it easier to use. Please see https://launch.usegalaxy.org/launch

ADD REPLY • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k

Hi, Jen:

Thanks so much for your reply! It's very helpful!

Best,

Wei-Ming

From: Jennifer Hillman Jackson on Galaxy Biostar [notifications@biostars.org] Sent: Tuesday, September 08, 2015 9:22 AM To: Yu, Wei-Ming Subject: [galaxy-biostar] A: RNA-Seq analysis using Galaxy in Amazon AWS

Activity on a post you are following on Galaxy Biostar

User Jennifer Hillman Jackson<http: biostar.usegalaxy.org="" u="" 254=""/> wrote Answer: RNA-Seq analysis using Galaxy in Amazon AWS<http: biostar.usegalaxy.org="" p="" 14029="" #14062="">:

Hello,

To launch your instance, use CloudLaunch found at http://usegalaxy.org under the top masthead menu under Cloud. A "large" instance could be enough, but if you do run into a memory issue, then scaling up to an instance type with high-memory configuration would be the solution.

Thanks for using Galaxy, Jen, Galaxy team

ADD REPLY • link written 3.2 years ago by wei-ming_yu • 0

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