AWS Setup Guide
SBCloud
The SBGrid AWS-based SBCloud platform is a cloud computing solution designed to provide researchers with scalable and flexible computational resources. By leveraging Amazon Web Services (AWS), SBCloud offers a robust infrastructure that supports a wide range of scientific applications and workflows. Key features include:
- Scalability: Easily scale resources up or down based on project needs.
- Flexibility: Access a variety of computational resources, including high-performance computing (HPC) instances, storage solutions, and specialized software.
- Cost-Effectiveness: Pay only for the resources you use, with the ability to optimize costs through various pricing models.
- Security: Benefit from AWS's comprehensive security measures to protect data and ensure compliance with industry standards.
- Collaboration: Facilitate collaboration among research teams by providing a centralized platform for data sharing and project management.
SBCloud is ideal for researchers who require powerful computational capabilities without the overhead of managing physical hardware. It enables efficient data processing, analysis, and storage, making it a valuable tool for advancing scientific research.
SBGrid in AWS EC2
SBGrid is easy to use on cloud resources. This is a short guide to using SBGrid on AWS.
Compatible AMIs
We recommend Rocky Linux 8 and Rocky Linux 9 AMIs for the SBGrid software stack. Amazon AMIs appear to work well, but are not routinely tested. Debian / Ubuntu AMIs should work but are untested. If you encounter any issues, please let us know.
For the example below we are using an Amazon Linux AMI, 2018.03.0 (HVM), SSD Volume Type - ami-14c5486b
Prerequisites
First login to your running instance and install tcsh. It is not provided on Linux by default but is required by several SBGrid applications.
Download the SBGrid command line interface
Download the SBGrid CLI installation manager.
curl -LO https://sbgrid.org/downloads/2.12.3/sbgrid-cli_2.12.3-linux.tar.gz
tar -zxvf sbgrid-cli_2.12.3.tar.gz
Activate your installation
If you don't have a username and key, register here: https://sbgrid.org/registration/register/
Install programs
Install RELION from the SBGrid collection using the SBGrid CLI application
Run your software
Initialize the environment, and your instance will be ready to use.
[ec2-user@ip-172-31-62-107 sbgrid-1.0.694-Linux]$ source /programs/sbgrid.shrc
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Software Support by SBGrid (www.sbgrid.org)
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SBGrid Announcements
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Your use of the applications contained in the /programs directory constitutes
acceptance of the terms of the SBGrid License Agreement included in the file
/programs/share/LICENSE. The applications distributed by SBGrid are licensed
exclusively to member laboratories of the SBGrid Consortium.
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SBGrid was developed with support from its members, Harvard Medical School,
HHMI, and NSF. If use of SBGrid compiled software was an important element
in your publication, please include the following reference in your work:
Software used in the project was installed and configured by SBGrid.
cite: eLife 2013;2:e01456, Collaboration gets the most out of software.
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SBGrid installation last updated: 2018-05-24
Please submit bug reports and help requests to: <bugs@sbgrid.org> or
<http://sbgrid.org/bugs>
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Capsule Status: Active
For additional information visit https://sbgrid.org/wiki/capsules
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Have problems? Want to learn more? Get in touch - bugs@sbgrid.org