AWS

SBGrid in AWS EC2

SBGrid is easy to use in on cloud resources. This is a short guide to using SBGrid on AWS.

SBGrid in AWS EC2

Compatible AMIs

     __|  __|_  )
     _|  (     /   Amazon Linux AMI
    ___|\___|___|

We recommend CentOS / RHEL 7 AMIs for the SBGrid software stack. Amazon AMIs appear to work well, but are not routinely tested. Debian / Ubuntu AMIs may work but are untested. If you have problems 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 titles.

sudo yum install tcsh

Download the SBGrid command line interface

Download the SBGrid CLI installation manager.

curl -LO https://sbgrid.org/downloads/latest/sbgrid-cli_linux.tar.gz
tar -zxvf sbgrid-cli_linux.tar.gz

Activate your installation

If you don't have a username and key, register here : https://sbgrid.org/registration/register/

./sbgrid-cli activate <site> <user> <key>

Install programs

relion as an example here -

./sbgrid-cli install relion

Run your software

Initialize the environment, and the instance is ready to go.

source /programs/sbgrid.shrc

[ec2-user@ip-172-31-62-107 sbgrid-1.0.694-Linux]$ source /programs/sbgrid.shrc
********************************************************************************
                  Software Support by SBGrid (www.sbgrid.org)
********************************************************************************
                              SBGrid Announcements
  - OpenMPI has been updated. RELION users please see
    <https://sbgrid.org/software/titles/relion> for mpirun version info.
********************************************************************************
 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.
********************************************************************************
 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.
********************************************************************************
 SBGrid installation last updated: 2018-05-24
 Please submit bug reports and help requests to:       <bugs@sbgrid.org>  or
                                                       <http://sbgrid.org/bugs>
********************************************************************************
 Capsule Status: Active
       For additional information visit https://sbgrid.org/wiki/capsules
********************************************************************************

Have problems? Want to learn more? Get in touch - bugs@sbgrid.org