Metadata-Version: 2.1
Name: accession
Version: 1.2.0
Summary: Tool to submit genomics pipeline outputs to the ENCODE Portal
Home-page: https://github.com/ENCODE-DCC/accession
Author: Paul Sud
Author-email: encode-help@lists.stanford.edu
License: MIT
Project-URL: Documentation, https://accession.readthedocs.io/en/latest/
Project-URL: Source Code, https://github.com/ENCODE-DCC/accession
Project-URL: Issue Tracker, https://github.com/ENCODE-DCC/accession/issues
Description: ==============
        accession
        ==============
        
        .. image:: https://img.shields.io/badge/code%20style-black-000000.svg
            :target: https://github.com/ambv/black
            :alt: Code Style: Black
        
        .. image:: https://img.shields.io/badge/License-MIT-blue.svg
           :target: https://lbesson.mit-license.org/
           :alt: License: MIT
        
        .. image:: https://circleci.com/gh/ENCODE-DCC/accession.svg?style=svg
            :target: https://circleci.com/gh/ENCODE-DCC/accession
            :alt: CircleCI status
        
        .. short-intro-begin
        
        ``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
        
        .. code-block:: console
        
            $ pip install accession
        
        Next, provide your API keys from the ENCODE portal:
        
        .. code-block:: console
        
            $ 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:
        
        .. code-block:: console
        
            $ 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.
        
        .. code-block:: console
        
            $ export DCC_LAB=XXXXXXXX
            $ export DCC_AWARD=yyyyyyyyyyy
        
        Usage
        ======
        
        .. code-block:: console
        
            $ accession --accession-metadata metadata.json \
                        --pipeline-type mirna \
                        --server dev
        
        Please see the `docs <https://accession.readthedocs.io/en/latest/#detailed-argument-description>`_ for greater detail on these input parameters.
        
        .. short-intro-end
        
        Project Information
        ====================
        
        ``accession`` is released under the `MIT <https://choosealicense.com/licenses/mit/>`_ license, documentation lives in `readthedocs <https://accession.readthedocs.io/en/latest/>`_, code is hosted on `github <https://github.com/ENCODE-DCC/accession>`_ and the releases on `PyPI <https://pypi.org/project/accession/>`_.
        
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.6
Description-Content-Type: text/x-rst
Provides-Extra: tests
Provides-Extra: docs
Provides-Extra: dev
