Tool to submit genomics pipeline outputs to the ENCODE Portal

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  • License: MIT License (MIT)
  • Author: Paul Sud
  • Requires: Python >=3.6
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Project description

Code Style: Black License: MIT CircleCI status

accession is a Python module and command line tool for submitting genomics pipeline analysis output files and metadata to the ENCODE Portal.

Installation

$ pip install accession

In addition to installing the module, make sure to provide your API keys from the ENCODE portal:

$ export DCC_API_KEY=XXXXXXXX
$ export DCC_SECRET_KEY=yyyyyyyyyyy

You will also need Google Application Credentials in your environment. Obtain and set your service account credentials:

$ export GOOGLE_APPLICATION_CREDENTIALS=<path_to_service_account_file>
Finally, it is highly recommended to set the DCC_LAB and DCC_AWARD environment variables for ease of use. These correspond to the lab and award identifiers given by the ENCODE portal, e.g. /labs/foo/ and U00HG123456, respectively.
$ export DCC_LAB=XXXXXXXX
$ export DCC_AWARD=yyyyyyyyyyy

Usage

$ accession --accession-metadata metadata.json \
            --pipeline-type mirna \
            --server dev \

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

Project Information

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

Project details

Verified details

These details have been verified by PyPI
Maintainers
Avatar for paulsud from gravatar.com paulsud Avatar for perna from gravatar.com perna Avatar for ulugbek from gravatar.com ulugbek

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Project links
Meta
  • License: MIT License (MIT)
  • Author: Paul Sud
  • Requires: Python >=3.6
Classifiers

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