Installation

Note: installation requires Python >= 3.8

$ pip install accession

Next, provide your API keys from the ENCODE portal:

$ export DCC_API_KEY=XXXXXXXX
$ export DCC_SECRET_KEY=yyyyyyyyyyy

$ export DCC_LAB=XXXXXXXX
$ export DCC_AWARD=yyyyyyyyyyy

$ gcloud auth login --no-launch-browser
$ gcloud auth application-default login --no-launch-browser

$ export ACCESSION_CLOUD_TASKS_QUEUE_NAME=my-queue
$ export ACCESSION_CLOUD_TASKS_QUEUE_REGION=us-west1

Usage

$ accession -m metadata.json \
            -p mirna \
            -s dev

Please see the docs for greater detail on these input parameters.

Deploying on Google Cloud

AWS Notes

To enable S3 to S3 copy from the pipeline buckets to the ENCODE buckets, ensure that the pipeline bucket policy grants read access to the ENCODE account. Here is an example policy:

{
    "Version": "2012-10-17",
    "Statement": [
        {
            "Sid": "DelegateS3AccessGet",
            "Effect": "Allow",
            "Principal": {
                "AWS": [
                    "arn:aws:iam::618537831167:root",
                    "arn:aws:iam::159877419961:root"
                ]
            },
            "Action": "s3:GetObject",
            "Resource": "arn:aws:s3:::PIPELINE-BUCKET/*"
        },
        {
            "Sid": "DelegateS3AccessList",
            "Effect": "Allow",
            "Principal": {
                "AWS": [
                    "arn:aws:iam::618537831167:root",
                    "arn:aws:iam::159877419961:root"
                ]
            },
            "Action": "s3:ListBucket",
            "Resource": "arn:aws:s3:::PIPELINE-BUCKET"
        }
    ]
}

Project Information

accession is released under the MIT license, documentation lives in readthedocs, code is hosted on github and the releases on PyPI.