deploy-cryosparc.sh
script via the CLI.us-east-1
~/.ssh
directory and is called key-cryoSPARC
.README.md
cryosparc-pcluster.config.template
deploy-cryosparc_v1.sh
install-cryosparc_v1.sh
vpc-cryosparc.template
cryosparc-test-data-np
for raw data. This S3 bucket will be linked to the Amazon FSx for Lustre service for high-performance read and write storage operations..tif
and .mrc
movies (multi-frame micrographs) to cryosparc-test-data-np
:vpc-cryosparc.template
is a CloudFormation template that deploys the VPC and subnets. As is, the script creates a VPC and two subnets. The subnet for the head instance is public, and the compute instances are placed in a private subnet. Outside the VPC, you can only log into the head instance in the public subnet (via SSH).pcluster
. First, confirm that you have the correct version installed.cryosparc-pcluster.config.template
in a text editor; here, provide the details of the cluster required to deploy and run the cryoSPARC workflow.cryosparc.config
file is created from the cryosparc.config.template
file (more on this later).cryosparc-pcluster.config.template
.aws_region_name
- the name of the regionkey_name
- key pair namepost_install
- the path to the install script that runs after the cluster is createds3_read_resource
- the S3 bucket with raw datavpc_id
- the VPC idmaster_subnet_id
- the subnet id where the head node residescompute_subnet_id
- the subnet id where the compute node residesdeploy-cryosparc.sh
fetches the remaining values about the networking infrastructure created by vpc-cryosparc.template
.cryosparc-pcluster.config.template
deploy-cryosparc.sh
vpc-cryosparc.template
--region
Region you want to deploy the cluster inValues=
type of instance--region
Region in which to deploy the cluster--cluster-name
Name of the cluster for identification purposes--az
AZ in which to deploy the cluster. Make sure that instance is available in the specified AZ. --data-bucket
Existing S3 bucket created earlier. This will be linked to the EC2 instance with Amazon FSx for Lustre. All movies will be uploaded here. --aws-key
Name (not the path) of the SSH key you created earlier--cryosparc-license-id
The license ID provided by Structura Bio for your cryoSPARC instancecryosparc.config
file is created from the cryosparc.config.template
file with all the values for the specified variables. This cryosparc.config
is specific to the cluster you just deployed. Check the cryosparc.config
file and ensure all the information is correct. Pay particular attention to the cluster cryosparc
, vpc cryosparc-vpc
and fsx cryosparc-fsx
sections.vpc-cryosparc.template
for later use. The deployment will take about 30 minutes. create-data-repository-task
command to export data from your Amazon FSx for Lustre file system to back to the data bucket:--file-system-id
The id for the Lustre file system created. Find this in the AWS console, under Amazon FSx.--paths
The paths of the directory or file you want to export relative to the mount point of the file system. If the mount point is /mnt/fsx
and /mnt/fsx/path1
is a directory or file on the file system you want to export, then provide path1
.