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.