Metadata-Version: 2.1
Name: macsyfinder
Version: 2.0rc1
Summary: MacSyFinder: Detection of macromolecular systems in protein datasets using systems modelling and similarity search
Home-page: https://github.com/gem-pasteur/macsyfinder/
Author: Sophie Abby, Bertrand Néron
Author-email: sophie.abby@univ-grenoble-alpes.fr, bneron@pasteur.fr
License: GPLv3
Download-URL: https://github.com/gem-pasteur/macsyfinder/
Description: # MacSyFinder
        
        [![Build Status](https://travis-ci.org/gem-pasteur/macsyfinder.svg?branch=master)](https://travis-ci.org/gem-pasteur/macsyfinder)
        [![Coverage Status](https://coveralls.io/repos/github/gem-pasteur/macsyfinder/badge.svg?branch=master)](https://coveralls.io/github/gem-pasteur/macsyfinder?branch=master)
        [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/macsyfinder)](https://pypi.org/project/macsyfinder/)
        [![Open Source License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://opensource.org/licenses/GPL-3.0)
        [![Doc](https://readthedocs.org/projects/macsyfinder/badge/?version=latest)](http://macsyfinder.readthedocs.org/en/latest/#)
        [![PyPI](https://img.shields.io/pypi/v/macsyfinder)](https://pypi.org/project/macsyfinder/)
        [![Docker Image Version (tag latest semver)](https://img.shields.io/docker/v/gempasteur/macsyfinder/latest)](https://hub.docker.com/repository/docker/gempasteur/macsyfinder)
        ![Conda](https://img.shields.io/conda/pn/bioconda/macsyfinder)
        
        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
        
        
        ## MacSyFinder is available on pypi
         
        [![PyPI](https://img.shields.io/pypi/v/macsyfinder)](https://pypi.org/project/macsyfinder/)
        
        ## Installation from distribution
        
        We encourage to install macsyfinder in a [virtualenv](https://virtualenv.pypa.io/en/latest/)
        
        After creating a virtualenv dedicated to macsyfinder and activating it
        
            python3 -m venv my_project
            cd my_project
            source bin/activate
        
        you can install macsyfinder as describe below.
            
        ### from pypi
        
            pip3 install macsyfinder==x.x
        
        where `x.x` is the version number
        
        ### from git repository
        
            git clone https://github.com/gem-pasteur/macsyfinder.git
            cd macsyfinder
            pip3 install .
            
        ### for developers
        
            git clone https://github.com/gem-pasteur/macsyfinder.git
            cd macsyfinder
            pip3 install .[dev]
         
        ## Unit tests 
        
            python3 setup.py test
            
        or 
            
            python3 tests/run_tests.py -vv
            
        or to run a specific test
        
            python3 tests/run_tests.py -vv tests/test_xxx.py
                
             
        ### with travis-ci
        
        [![Build Status](https://travis-ci.org/gem-pasteur/macsyfinder.svg?branch=master)](https://travis-ci.org/gem-pasteur/macsyfinder)
        [![Coverage Status](https://coveralls.io/repos/github/gem-pasteur/macsyfinder/badge.svg?branch=master)](https://coveralls.io/github/gem-pasteur/macsyfinder?branch=master)
        
        ## Documentation
        
        You will find complete documentation for setting up your project on readthedocs
        
        [![Doc](https://readthedocs.org/projects/macsyfinder/badge/?version=latest)](http://macsyfinder.readthedocs.org/en/latest/#)
        
        ## Docker
        
        MacSyFinder is also available as [Docker container](https://hub.docker.com/repository/docker/gempasteur/macsyfinder)
        
        ### how to use macsyfinder container with docker
        
        The computaion are perform under `msf` user in `/home/msf` inside the container.
        So You have to mount a directory from the host in the container to exchange data (inputs data, and results)
        from the host and the container.
        The shared directory must be writable by the `msf` user or overwrite the user in the container by your id (see example below)
        
            mkdir shared_dir
            cd shared_dir
            docker run -v ${PWD}/:/home/msf -u $(id -u ${USER}):$(id -g ${USER})  macsyfinder:2.0rc1  --db-type gembase --models-dir=/models/ --models  TFF-SF Archaeal-T4P ComM MSH T2SS T4bP T4P Tad --sequence-db my_genome.fasta -w 12
        
        ### how to use with singularity
        
        As the docker image is registered in docker hub you can also use it directly with [Singularity](https://sylabs.io/docs/).
        Unlike docker you have not to worry about shared directory, your `home` and `/tmp` are automatically shared.
        
            singularity run -H ${HOME} docker://gempasteur/macsyfinder:2.0rc1 --db-type gembase --models-dir=/models/ --models  TFF-SF Archaeal-T4P ComM MSH T2SS T4bP T4P Tad --sequence-db my_genome.fasta -w 12
        
        ## Licence:
        
        MacSyFinder is developed and released under [![Open Source License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://opensource.org/licenses/GPL-3.0)
        
        ## Contributing 
        
        We encourage contributions, bug report, enhancement ... 
        
        But before to do that, we encourage to read [the contributing guide](CONTRIBUTING.md).
        
        ## Contributors
        
        [List of all people who participated in the macsyfinder project](CONTRIBUTORS.md).
        
        ## 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.
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: dev
