MacSyFinder 2.0rc4

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

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

Docker

MacSyFinder is also available as Docker container

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})  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

how to use with singularity

As the docker image is registered in docker hub you can also use it directly with Singularity. 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

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.