Image-based Profiling for VarChAMP

This repository was derived from a template repository located at https://github.com/cytomining/profiling-template. The purpose of the repository is to weld together a versioned data processing pipeline with versioned processed output data for a single image-based profiling experiment.

Notes

To download the data in this repo, first, clone this repo

git clone [email protected]:broadinstitute/2021_09_01_VarChAMP-data.git

then, download the profiles

cd 2021_09_01_VarChAMP-data
dvc pull

AWS configuration

The DVC cache is stored in an AWS S3 bucket. To access the files stored via DVC, you will need to created a IAM user with the AmazonS3ReadOnlyAccess policy attached:

{
    "Version": "2012-10-17",
    "Statement": [
        {
            "Effect": "Allow",
            "Action": [
                "s3:Get*",
                "s3:List*",
                "s3-object-lambda:Get*",
                "s3-object-lambda:List*"
            ],
            "Resource": "*"
        }
    ]
}