Metadata-Version: 2.1
Name: accession
Version: 1.0.0
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
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
Requires-Dist: requests
Requires-Dist: encode-utils (==2.5.0)
Requires-Dist: google-cloud-storage
Requires-Dist: attrs
Provides-Extra: dev
Requires-Dist: sphinx ; extra == 'dev'
Requires-Dist: pytest ; extra == 'dev'
Requires-Dist: pytest-cov ; extra == 'dev'
Requires-Dist: pytest-mock ; extra == 'dev'
Requires-Dist: docker ; extra == 'dev'
Requires-Dist: pre-commit ; extra == 'dev'
Provides-Extra: docs
Requires-Dist: sphinx ; extra == 'docs'
Provides-Extra: tests
Requires-Dist: pytest ; extra == 'tests'
Requires-Dist: pytest-cov ; extra == 'tests'
Requires-Dist: pytest-mock ; extra == 'tests'
Requires-Dist: docker ; extra == 'tests'

==============
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
=============

.. code-block:: console

    $ pip install accession

In addition to installing the module, make sure to 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 `Google Application Credentials <https://cloud.google.com/video-intelligence/docs/common/auth#set_up_a_service_account/>`_ in your environment. Obtain and set your service account credentials:

.. code-block:: console

    $ 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.

.. 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/>`_.


