OpenCRAVAT

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

fs = DagsHubFilesystem(".", repo_url="https://dagshub.com/DagsHub-Datasets/open-cravat-dataset")

fs.listdir("s3://opencravat-store-aws")

Description:

OpenCRAVAT is a module variant annotation tool developed by KarchinLab at Johns Hopkins. This dataset is a mirror of the OpenCRAVAT store available at https://store.opencravat.org. You can configure OpenCRAVAT to use this mirror by editing the "cravat-system.yml" file. The path to this file is in the first output line of the command "oc config system". In that file, change the value of "store_url" to "https://opencravat-store-aws.s3.amazonaws.com".

Contact:

OpenCRAVAT is a module variant annotation tool developed by KarchinLab at Johns Hopkins. This dataset is a mirror of the OpenCRAVAT store available at https://store.opencravat.org. You can configure OpenCRAVAT to use this mirror by editing the "cravat-system.yml" file. The path to this file is in the first output line of the command "oc config system". In that file, change the value of "store_url" to "https://opencravat-store-aws.s3.amazonaws.com".

Update Frequency:

Data is mirrored daily. Update frequencies of individual annotators depend on the update schedule of the source data.

Managed By:

KarchinLab, Potomac IT Group

Resources:

1. resource:

   • Description: OpenCRAVAT Store US
   • ARN: arn:aws:s3:::opencravat-store-aws
   • Region: us-east-1
   • Type: S3 Bucket

2. resource:

   • Description: OpenCRAVAT Store EU
   • ARN: arn:aws:s3:::opencravat-store-eu-west-2
   • Region: eu-west-2
   • Type: S3 Bucket

Tags:

aws-pds, genetic, genomic, life sciences, variant annotation, sqlite, tertiary analysis

Tutorials:

1. tutorial:
   • Title: Changing the OpenCRAVAT store url
   • URL: https://open-cravat.readthedocs.io/en/latest/AWS-OpenData.html
   • AuthorName: Kyle Moad

Tools & Applications:

1. tools & applications:
   • Title: OpenCRAVAT
   • URL: https://opencravat.org
   • AuthorName: Karchinlab
   • AuthorURL: https://karchinlab.org