Cloud Computing for the Microbiome Workshop Notes

Comprehensive documentation can be found at CloudMan.

Quick start

Start at Galaxy Cloud Launch Enter AWS Credentials (AWS Key ID and Secret)

  • Cluster Name - A name for your cluster.
  • Password - A password for the administrative functions of your cluster.
  • Key ID - AWS Key ID (The short part)
  • Secret Key - AWS Secret Key (The long part)
  • Instance Type - The type of EC2 instance you would like. m1.large or higher recommended.

Navigate to the URL presented on the confirmation page to configure your cluster

  • To create an exact copy of the instance from our workshop demo, click "advanced options", and enter the Instance Share String below
  • OR, to create a regular Galaxy cluster, just enter how much space(in gigabytes) you'd like to have to work with.

Instance Share String: cm-e49d0cbc21a77988d38b0d13890eee8f/shared/2012-04-03--19-54/

At this point, just wait a few seconds and you're ready to go when the "Access Galaxy" button lights up.

Additional Links





For Advanced Users - Getting the workshop data (Titus' snapshot) in to Galaxy

Documentation covering Galaxy Data Libraries can be found at Admin/DataLibraries/Libraries

Specific documentation covering options for uploading to be libraries can be found at Admin/DataLibraries/UploadingLibraryFiles

This currently requires creating a volume from the AWS Console and mounting via the instance's shell (via ssh).

  • From AWS, note the Availability Zone of your EC2 instance, then click Elastic Block Store -> Volumes -> Create Volume, then enter the following parameters:

    • Size: 1 TiB
    • Availability Zone: Same as your EC2 Instance
    • Snapshot: snap-17f4c06d
  • With the new volume checked, click More... -> Attach Volume, select your instance and set the device (the default device name filled in to the dialog once you select your instance is acceptable).
  • Log in to your instance using SSH: ssh -i /path/to/your/ecs_ssh_private_key ubuntu@ec2-1-2-3-4.compute-1.amazonaws.com
  • Become root: sudo -i
  • Mount the volume: mkdir /mnt/workshopData; mnt /dev/sdf /mnt/workshopData
  • From the Galaxy Admin interface (if you have not yet configured an account to be a Galaxy administrator, you can do so at http://ec2-1-2-3-4.compute-1.amazonaws.com/cloud/root/admin ), click Manage data libraries -> Create new data library.
  • Enter a name and optional description/synopsis for the library, and click Create.
  • In your new library, click Add datasets.
  • From Upload option, select Upload files from filesystem paths.
  • In Paths to upload, enter the path(s) (/mnt/workshopData/...) to files or directories that you would like to import.
  • Click Upload to library.