Installation

MacSyFinder works with models for macromolecular systems that are not shipped with it, you have to install them separately. See the macsydata section below.

MacSyFinder dependencies

Python version >=3.7 is required to run MacSyFinder: https://docs.python.org/3.7/index.html

MacSyFinder has one program dependency:

The hmmsearch program should be installed (e.g., in the PATH) in order to use MacSyFinder. Otherwise, the paths to this executable must be specified in the command-line: see the command-line options.

MacSyFinder also relies on four Python library dependencies:

  • colorlog
  • pyyaml
  • packaging
  • networkx

These dependencies will be automatically retrieved and installed when using pip for installation (see below).

MacSyFinder Installation procedure

It is recommended to use pip to install the MacSyFinder package.

Archive overview

  • doc => the documentation in html and pdf
  • etc => a template of macsyfinder configuration file
  • test => all what is needed for unitary tests
  • macsypy => the macsyfinder python library
  • setup.py => the installation script
  • requirements.txt => the python dependencies
  • requirements_dev.txt => the python dependencies for developers
  • COPYING => the licensing
  • COPYRIGHT => the copyright
  • README.md => very brief macsyfinder overview
  • CONTRIBUTORS => list of people who contributed to the code

Installation steps:

Make sure every required dependency/software is present.

By default MacSyFinder will try to use hmmsearch in your PATH. If hmmsearch is not in the PATH, you have to set the absolute path to hmmsearch in a configuration file or in the command-line upon execution. If the tools are not in the path, some test will be skipped and a warning will be raised.

Perform the installation.

pip install --no-binary macsyfinder macsyfinder

If you do not have the privileges to perform a system-wide installation, you can either install it in your home directory or use a virtual environment.

installation in your home directory
pip install --user --no-binary macsyfinder macsyfinder
installation in a virtualenv
python3.7 -m venv macsyfinder
cd macsyfinder
source bin/activate
pip install --no-binary macsyfinder macsyfinder

To exit the virtualenv just execute the deactivate command. To run macsyfinder, you need to activate the virtualenv:

source macsyfinder/bin/activate

Then run macsyfinder or macsydata.

Note

Super-user privileges (i.e., sudo) are necessary if you want to install the program in the general file architecture.

Note

If you do not have the privileges, or if you do not want to install MacSyFinder in the Python libraries of your system, you can install MacSyFinder in a virtual environment (http://www.virtualenv.org/).

Warning

When installing a new version of MacSyFinder, do not forget to uninstall the previous version installed !

Uninstalling MacSyFinder

To uninstall MacSyFinder (the last version installed), run:

(sudo) pip uninstall macsyfinder

If you install it in a virtualenv, just delete the virtual environment. For instance if you create a virtualenv name macsyfinder:

python3.7 -m venv macsyfinder

To delete it, remove the directory:

rm -R macsyfinder

Models installation with macsydata

Once MacSyFinder is installed you have access to an utility program to manage the models: macsydata

This script allows to search, download, install and get information from MacSyFinder models stored on github or locally installed. The general syntax for macsydata is:

macsydata <general options> <subcommand> <sub command options> <arguments>

To list all models available:

macsydata available

To search for models:

macsydata search TXSS

you can also search in models description:

macsydata search -S secretion

To install a model package:

macsydata install <model name>

To install a model when you have not the right to install it system-wide:

macsydata install --user <model name>

To know how to cite a model package:

macsydata cite <model name>

To list all macsydata subcommands:

macsydata --help

To list all available options for a subcommand:

macsydata <subcommand> --help