File: README.md

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macsyfinder 1.0.5-3
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MacSyFinder
===========

[![pipeline status](https://gitlab.pasteur.fr/gem/MacSyFinder/badges/master/pipeline.svg)]
(https://gitlab.pasteur.fr/gem/MacSyFinder/commits/master)
[![coverage report](https://gitlab.pasteur.fr/gem/MacSyFinder/badges/master/coverage.svg)]
(https://gitlab.pasteur.fr/gem/MacSyFinder/commits/master)
[![Documentation]()https://img.shields.io/badge/style-plastic-blue.svg?style=plastic

MacSyFinder - Detection of macromolecular systems in protein datasets using systems modelling and similarity search.



Citation
-------- 
Abby SS, Néron B, Ménager H, Touchon M, Rocha EPC (2014). MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems. PLoS ONE 9(10): e110726. doi:10.1371/journal.pone.0110726
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0110726


Download distribution
---------------------
 
[ ![Download](https://api.bintray.com/packages/gem-pasteur/MacSyFinder/macsyfinder/images/download.svg) ](https://bintray.com/gem-pasteur/MacSyFinder/macsyfinder/_latestVersion)


Installation from distribution
------------------------------

1. Uncompress and untar the package:

```bash
tar -xzf macsyfinder-x.x.tar.gz
```

2. Go to the MacSyFinder directory
 
```bash
cd macsyfinder-x.x
```

3. Build 

```bash
python setup.py build
```

4. Test    

```bash
python setup.py test -vv
```

5. Install

```bash
sudo python setup.py install
```

    To see all installation options "python setup.py --help"

See the INSTALL file for more details.


Installation from repository
----------------------------

 Please be careful, MacSyView has its own repository: https://github.com/gem-pasteur/macsyview
 
 
 
Unit tests with Travis-CI
-------------------------
 [![Build Status](https://travis-ci.org/gem-pasteur/macsyfinder.svg?branch=master)](https://travis-ci.org/gem-pasteur/macsyfinder)

Unit tests with gitlab-ci
-------------------------
[![pipeline status](https://gitlab.pasteur.fr/gem/MacSyFinder/badges/master/pipeline.svg)](https://gitlab.pasteur.fr/gem/MacSyFinder/commits/master)  
[![coverage report](https://gitlab.pasteur.fr/gem/MacSyFinder/badges/master/coverage.svg)](http://gem.pages.pasteur.fr/MacSyFinder/htmlcov/index.html)



Documentation
-------------

You will find complete documentation for setting up your project.
for the development version on gitlab pages

[![Doc] (https://img.shields.io/badge/docs-passed-brightgreen.svg)](http://gem.pages.pasteur.fr/MacSyFinder/)


for public version on readthedocs

[![Doc] (https://readthedocs.org/projects/macsyfinder/badge/?version=latest)](http://macsyfinder.readthedocs.org/en/latest/#)


Note
----

The `setsid` binary in *utils* directory is used only for functional tests on macosx. 
The binary has been build using the [setsid-macosx](https://github.com/tzvetkoff/setsid-macosx) project.