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Tool to submit genomics pipeline outputs to the ENCODE Portal

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

Note: intallation requires Python >= 3.6

$ pip install accession

Next, provide your API keys from the ENCODE portal:

$ export DCC_API_KEY=XXXXXXXX
$ export DCC_SECRET_KEY=yyyyyyyyyyy

You will also need to authenticate with Google Cloud if using WDL metadata from pipeline runs on Google Cloud. Run the following two commands and follow the prompts:

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


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