Commit 95ad7a15 authored by Fabrice  ALLAIN's avatar Fabrice ALLAIN
Browse files

Merge branch 'master' into 3-uniformization-of-docs-between-aria-and-conbox

parents 1adeca84 082e6ee9
......@@ -33,7 +33,7 @@ coverage:
stage: coverage
image: registry-gitlab.pasteur.fr/bis-aria/ariaec:$CI_BUILD_REF_NAME
script:
- pytest --cov=aria --cov-report html
- pytest --cov=aria --cov-report html --cov-report term
coverage: '/TOTAL.+ ([0-9]{1,3}%)/'
artifacts:
paths:
......
## de Novo Ambiguous Restraints for Iterative Assignment
**A pipeline for automated de novo contact map assignment**
[![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](https://www.python.org/) library that provides *de novo* structure prediction
based on [ARIA](http://aria.pasteur.fr/) pipeline and evolutionary restraints inferred from co-evolution.
The package add a new command line interface aside the usual ARIA commands in
order to convert data, setup an ARIA project with evolutionary restraints,
analyze contact maps or protein structures or generate statistics from a culled
list of PDB files.
## 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)
Then the easiest solution is to call the **pip** command below :
`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)
**ARIA contains patches for CNS-solve which needs to be compiled after the installation. Please follow [post installation instructions](http://bis-aria.pages.pasteur.fr/ariaec/installation.html#post-installation-instructions).**
## Contributing
Please read [guidelines for contributing](https://gitlab.pasteur.fr/bis-aria/ariaec/blob/master/CONTRIBUTING.md) for any
suggestions or bug report.
=====================================================
de Novo Ambiguous Restraints for Iterative Assignment
=====================================================
**A pipeline for automated de novo contact map assignment**
.. 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
**ariaec** is a Python_ library that provides *de novo* structure prediction
based on ARIA_ pipeline and evolutionary restraints inferred from co-evolution.
The package add a new command line interface aside the usual ARIA commands in
order to convert data, setup an ARIA project with evolutionary restraints,
analyze contact maps or protein structures and generate statistics from a culled
list of PDB files.
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)
Then the easiest solution is to call the **pip** command below :
``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>`_.
Contributing
------------
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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