MacSyFinder 2.0rc1

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

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

Installation from distribution

We encourage to install macsyfinder in a virtualenv

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

Documentation

You will find complete documentation for setting up your project on readthedocs

Licence:

MacSyFinder is developed and released under

Contributing

We encourage contributions, bug report, enhancement ...

But before to do that, we encourage to read the contributing guide.

Contributors

List of all people who participated in the macsyfinder project.

Note

The setsid binary in utils directory is used only for functional tests on macosx. The binary has been build using the setsid-macosx project.