Commit e2dffc37 authored by Fabrice  ALLAIN's avatar Fabrice ALLAIN
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Update README.rst to README.md

parent c84bc317
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de Novo Ambiguous Restraints for Iterative Assignment
=====================================================
## de Novo Ambiguous Restraints for Iterative Assignment
**A pipeline for automated de novo contact map assignment**
.. image:: https://img.shields.io/readthedocs/pip.svg
:target: http://bis-aria.pages.pasteur.fr/ariaec
:alt: Read the Doc
.. image:: https://gitlab.pasteur.fr/bis-aria/ariaec/badges/master/pipeline.svg
:target: https://gitlab.pasteur.fr/bis-aria/ariaec/commits/master
:alt: Pipeline status
.. image:: https://gitlab.pasteur.fr/bis-aria/ariaec/badges/master/coverage.svg
:target: https://gitlab.pasteur.fr/bis-aria/ariaec/commits/master
:alt: Coverage report
.. image:: https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtl589-blue.svg
:target: https://doi.org/10.1093/bioinformatics/btl589
:alt: DOI status
[![pipeline status](https://gitlab.pasteur.fr/bis-aria/ariaec/badges/master/pipeline.svg)](https://gitlab.pasteur.fr/bis-aria/ariaec/commits/master)
[![coverage report](https://gitlab.pasteur.fr/bis-aria/ariaec/badges/master/coverage.svg)](https://gitlab.pasteur.fr/bis-aria/ariaec/commits/master)
[![documentation](https://img.shields.io/readthedocs/pip.svg)](http://bis-aria.pages.pasteur.fr/ariaec)
[![aria paper](https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtl589-blue.svg)](https://doi.org/10.1093/bioinformatics/btl589)
**ariaec** is a Python_ library that provides *de novo* structure prediction
based on ARIA_ pipeline and evolutionary restraints inferred from co-evolution.
......@@ -31,48 +17,29 @@ analyze contact maps or protein structures and generate statistics from a culled
list of PDB files.
Quick Start
-----------
## Quick Start
Be sure to check if the following packages are correctly installed with
your python installation or virtual environment.
* **pip** (>= 9.0)
* **setuptools** (>= 18.0)
* **numpy** (>= 1.11)
* **cns-solve** (1.21)
- **pip** (>= 9.0)
- **setuptools** (>= 18.0)
- **numpy** (>= 1.11)
- **cns-solve** (1.21)
Then the easiest solution is to call the **pip** command below :
``pip install git+https://gitlab.pasteur.fr/bis-aria/ariaec``
`pip install git+https://gitlab.pasteur.fr/bis-aria/ariaec`
For more information about installation and usage, please refer to the
`ARIAEC documentation <http://bis-aria.pages.pasteur.fr/ariaec>`_.
.. raw:: html
<div class="alert alert-warning">
[ARIAEC documentation](http://bis-aria.pages.pasteur.fr/ariaec)
This package contains patches for **CNS-solve** which needs to be compiled
after the installation. Please follow post installation instruction
before using ``aria2`` pipeline.
.. raw:: html
</div>
{: .alert .alert-warning .text-center}
Contributing
------------
## Contributing
Please read `guidelines for contributing <https://gitlab.pasteur.fr/bis-aria/ariaec/blob/master/CONTRIBUTING.md>`_ for any
Please read [guidelines for contributing](https://gitlab.pasteur.fr/bis-aria/ariaec/blob/master/CONTRIBUTING.md) for any
suggestions or bug report.
.. Hyperlinks
.. _ZIP: https://gitlab.pasteur.fr/bis-aria/ariaec/repository/master/archive.zip
.. _TAR: https://gitlab.pasteur.fr/bis-aria/ariaec/repository/master/archive.tar
.. _Gitlab: https://gitlab.pasteur.fr/bis-aria/ariaec
.. _ARIA: http://aria.pasteur.fr
.. _Python: https://www.python.org
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