Metadata-Version: 2.1
Name: resolwe-bio
Version: 36.1.0
Summary: Bioinformatics pipelines for the Resolwe platform
Home-page: https://github.com/genialis/resolwe-bio
Author: Genialis, Inc.
Author-email: dev-team@genialis.com
License: Apache License (2.0)
Keywords: bioinformatics resolwe bio pipelines dataflow django
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Web Environment
Classifier: Framework :: Django
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.6, <3.9
Description-Content-Type: text/x-rst
Requires-Dist: Django (~=2.2.0)
Requires-Dist: djangorestframework (~=3.9.0)
Requires-Dist: django-filter (~=2.0.0)
Requires-Dist: resolwe (==27.*,>=27.0a1)
Requires-Dist: urllib3 (~=1.24.2)
Requires-Dist: wrapt (~=1.11.1)
Provides-Extra: docs
Requires-Dist: Sphinx (~=1.5.6) ; extra == 'docs'
Requires-Dist: sphinx-rtd-theme ; extra == 'docs'
Requires-Dist: docutils (==0.15.2) ; extra == 'docs'
Requires-Dist: pyasn1 (>=0.4.8) ; extra == 'docs'
Provides-Extra: package
Requires-Dist: twine ; extra == 'package'
Requires-Dist: wheel ; extra == 'package'
Provides-Extra: test
Requires-Dist: black ; extra == 'test'
Requires-Dist: flake8 (~=3.7.0) ; extra == 'test'
Requires-Dist: isort (~=4.3.12) ; extra == 'test'
Requires-Dist: pydocstyle (~=3.0.0) ; extra == 'test'
Requires-Dist: tblib (~=1.3.0) ; extra == 'test'
Requires-Dist: check-manifest ; extra == 'test'
Requires-Dist: setuptools-scm ; extra == 'test'
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Requires-Dist: six (==1.12) ; extra == 'test'
Requires-Dist: build (==0.2.1) ; extra == 'test'

======================
Resolwe Bioinformatics
======================

|build| |coverage| |docs| |pypi_version| |pypi_pyversions|

.. |build| image:: https://public.ci.genialis.io/buildStatus/icon/resolwe-bio/master
    :target: https://ci.genialis.io/blue/organizations/jenkins/resolwe-bio/activity
    :alt: Build Status

.. |coverage| image:: https://img.shields.io/codecov/c/github/genialis/resolwe-bio/master.svg
    :target: http://codecov.io/github/genialis/resolwe-bio?branch=master
    :alt: Coverage Status

.. |docs| image:: https://readthedocs.org/projects/resolwe-bio/badge/?version=latest
    :target: http://resolwe-bio.readthedocs.io/
    :alt: Documentation Status

.. |pypi_version| image:: https://img.shields.io/pypi/v/resolwe-bio.svg
    :target: https://pypi.python.org/pypi/resolwe-bio
    :alt: Version on PyPI

.. |pypi_pyversions| image:: https://img.shields.io/pypi/pyversions/resolwe-bio.svg
    :target: https://pypi.python.org/pypi/resolwe-bio
    :alt: Supported Python versions

.. |pypi_downloads| image:: https://img.shields.io/pypi/dm/resolwe-bio.svg
    :target: https://pypi.python.org/pypi/resolwe-bio
    :alt: Number of downloads from PyPI

Bioinformatics pipelines for the Resolwe_ dataflow package for `Django
framework`_.

.. _Resolwe: https://github.com/genialis/resolwe
.. _Django framework: https://www.djangoproject.com/


Docs & Help
===========

Read about getting started and how to write `processes` in the documentation_.

To chat with developers or ask for help, join us on Slack_.

.. _documentation: http://resolwe-bio.readthedocs.io/
.. _Slack: http://resolwe.slack.com/


Install
=======

Prerequisites
-------------

Make sure you have Python_ 3.6 installed on your system. If you don't have it
yet, follow `these instructions
<https://docs.python.org/3/using/index.html>`__.

Resolwe requires PostgreSQL_ (9.4+). Many Linux distributions already include
the required version of PostgreSQL (e.g. Fedora 22+, Debian 8+, Ubuntu 15.04+)
and you can simply install it via distribution's package manager.
Otherwise, follow `these instructions
<https://wiki.postgresql.org/wiki/Detailed_installation_guides>`__.

Additionally, installing some (indirect) dependencies from PyPI_ will require
having a C compiler (e.g. GCC_) as well as Python development files installed
on the system.

Note
^^^^

The preferred way to install the C compiler and Python development files is to
use your distribution's packages, if they exist. For example, on a
Fedora/RHEL-based system, that would mean installing ``gcc`` and
``python3-devel`` packages.

.. _Python: https://www.python.org/
.. _PostgreSQL: http://www.postgresql.org/
.. _PyPi: https://pypi.python.org/
.. _GCC: https://gcc.gnu.org/

Using PyPI_
-----------

.. code::

    pip install resolwe-bio

To install a pre-release, use:

.. code::

    pip install --pre resolwe-bio

Using source on GitHub_
-----------------------

.. code::

   pip install --pre https://github.com/genialis/resolwe-bio/archive/<git-tree-ish>.tar.gz

where ``<git-tree-ish>`` can represent any commit SHA, branch name, tag name,
etc. in `Resolwe Bioinformatics' GitHub repository`_. For example, to install
the latest Resolwe Bioinformatics from the ``master`` branch, use:

.. code::

   pip install --pre https://github.com/genialis/resolwe-bio/archive/master.tar.gz

.. _`Resolwe Bioinformatics' GitHub repository`: https://github.com/genialis/resolwe-bio/
.. _GitHub: `Resolwe Bioinformatics' GitHub repository`_


Contribute
==========

We welcome new contributors. To learn more, read Contributing_ section of the
documentation.

.. _Contributing: http://resolwe-bio.readthedocs.io/en/latest/contributing.html


