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 Hmmer program, version 3.1 or greater (http://hmmer.org/).
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