Bioinformatics pipelines for the Resolwe platform.
Project description
======================
Resolwe Bioinformatics
======================
|build| |docs| |pypi_version| |pypi_pyversions|
.. |build| image:: https://travis-ci.org/genialis/resolwe-bio.svg?branch=master
:target: https://travis-ci.org/genialis/resolwe-bio
:alt: Build 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-hypernode.com/pypi/resolwe-bio
:alt: Version on PyPI
.. |pypi_pyversions| image:: https://img.shields.io/pypi/pyversions/resolwe-bio.svg
:target: https://pypi-hypernode.com/pypi/resolwe-bio
:alt: Supported Python versions
.. |pypi_downloads| image:: https://img.shields.io/pypi/dm/resolwe-bio.svg
:target: https://pypi-hypernode.com/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_ (2.7 or 3.4+) 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 the ``psycopg2`` dependency from PyPI_ will require
having a C compiler (e.g. GCC_) as well as Python and PostgreSQL development
files installed on the system.
Note
^^^^
The preferred way to install the C compiler and Python and PostgreSQL
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``,
``python-devel``/``python3-devel`` and ``postgresql-devel`` packages.
.. _Python: https://www.python.org/
.. _PostgreSQL: http://www.postgresql.org/
.. _PyPi: https://pypi-hypernode.com/
.. _GCC: https://gcc.gnu.org/
>From PyPI_
----------
.. code::
pip install resolwe-bio
>From source
-----------
.. code::
pip install 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 https://github.com/genialis/resolwe-bio/archive/master.tar.gz
.. _`Resolwe Bioinformatics' GitHub repository`: https://github.com/genialis/resolwe-bio/
Contribute
==========
We welcome new contributors. To learn more, read Contributing_ section of the
documentation.
.. _Contributing: http://resolwe-bio.readthedocs.io/en/latest/contributing.html
Resolwe Bioinformatics
======================
|build| |docs| |pypi_version| |pypi_pyversions|
.. |build| image:: https://travis-ci.org/genialis/resolwe-bio.svg?branch=master
:target: https://travis-ci.org/genialis/resolwe-bio
:alt: Build 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-hypernode.com/pypi/resolwe-bio
:alt: Version on PyPI
.. |pypi_pyversions| image:: https://img.shields.io/pypi/pyversions/resolwe-bio.svg
:target: https://pypi-hypernode.com/pypi/resolwe-bio
:alt: Supported Python versions
.. |pypi_downloads| image:: https://img.shields.io/pypi/dm/resolwe-bio.svg
:target: https://pypi-hypernode.com/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_ (2.7 or 3.4+) 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 the ``psycopg2`` dependency from PyPI_ will require
having a C compiler (e.g. GCC_) as well as Python and PostgreSQL development
files installed on the system.
Note
^^^^
The preferred way to install the C compiler and Python and PostgreSQL
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``,
``python-devel``/``python3-devel`` and ``postgresql-devel`` packages.
.. _Python: https://www.python.org/
.. _PostgreSQL: http://www.postgresql.org/
.. _PyPi: https://pypi-hypernode.com/
.. _GCC: https://gcc.gnu.org/
>From PyPI_
----------
.. code::
pip install resolwe-bio
>From source
-----------
.. code::
pip install 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 https://github.com/genialis/resolwe-bio/archive/master.tar.gz
.. _`Resolwe Bioinformatics' GitHub repository`: https://github.com/genialis/resolwe-bio/
Contribute
==========
We welcome new contributors. To learn more, read Contributing_ section of the
documentation.
.. _Contributing: http://resolwe-bio.readthedocs.io/en/latest/contributing.html
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