Installation

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

MacSyLib dependencies

Python version >=3.10 is required to run MacSyLib: https://docs.python.org/3.10/index.html

MacSyLib has one program dependency:

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

MacSyLib also relies on six Python library dependencies:

  • colorlog

  • colorama

  • pyyaml

  • packaging

  • networkx

  • pandas

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

Note

If you intend to build and distribute new models you will need some other dependencies see modeler guide for installation.

Note

If you want to contribute to the MacSyLib code, check the guide lines (CONTRIBUTING) and specific procedure for developer installation.

MacSyLib Installation procedure

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

Archive overview

  • doc => The documentation in html and pdf

  • test => All what is needed for unitary tests

  • src/macsylib => The macsylib python library

  • setup.py => The installation script (to include documentation)

  • pyproject.toml => The project installation build tool

  • COPYING => The licensing

  • COPYRIGHT => The copyright

  • README.md => Very brief MacSyLib overview

  • CONTRIBUTORS => List of people who contributed to the code

  • CONTRIBUTING => The guide lines to contribute to the code

Installation steps:

Make sure every required dependency/software is present.

By default MacSyLib 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.

python3 -m pip install macsylib

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
python3 -m pip install --user macsylib
installation in a virtualenv
python3 -m venv macsylib
cd macsylib
source bin/activate
python3 -m pip install macsylib

To exit the virtualenv just execute the deactivate command. To use macsylib, you need to activate the virtualenv:

source macsylib/bin/activate

Then use macsylib as python library or the msl_data command line tool.

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 MacSyLib in the Python libraries of your system, you can install MacSyLib in a virtual environment (http://www.virtualenv.org/).

Warning

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

Uninstalling MacSyLib

To uninstall MacSyLib (the last version installed), run

(sudo) pip uninstall macsylib

If you have installed it in a virtualenv, just delete the virtual environment. For instance if you create a virtualenv name macsylib

python3 -m venv macsylib

To delete it, remove the directory

rm -R macsylib

From Conda/Mamba

From version 1.0, MacSyLib is packaged for Conda/Mamba .. code-block:: text

mamba install -c macsylib=x.x

Where x.x is the macsylib version you want to install

Models installation with msl_data

Once MacSyLib is installed you have access to an utility program to manage the models: msl_data

This script allows to search, download, install and get information from MacSyLib models stored on github (https://github.com/macsy-models) or locally installed. The general syntax for msl_data is:

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

To list all models available on macsy-models:

msl_data available

To search for models on macsy-models:

msl_data search TXSS

you can also search in models description:

msl_data search -S secretion

To install a model package:

msl_data install <model name>

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

To install it in your home (./macsylib/data):

msl_data install --user <model name>

To install it in any directory:

msl_data install --target <model dir> <model_name>

To know how to cite a model package:

msl_data cite <model name>

To show the name of the models and the structure of installed model package:

msl_data show <model package name>

for instance msl_data show TXSScan

TXSScan
    ├-archaea
    │   └-Archaeal-T4P
    └-bacteria
         ├-diderm
         │   ├-Flagellum
         │   ├-MSH
         │   ├-T1SS
         │   ├-T2SS
         │   ├-T3SS
         │   ├-T4aP
         │   ├-T4bP
         │   ├-T5aSS
         │   ├-T5bSS
         │   ├-T5cSS
         │   ├-T6SSi
         │   ├-T6SSii
         │   ├-T6SSiii
         │   ├-T9SS
         │   ├-Tad
         │   ├-pT4SSi
         │   └-pT4SSt
         └-monoderm
              └-ComM

TXSScan (1.1.3) : 19 models

To show the model definition:

msl_data definition <package or subpackage> model1 [model2, ...]

for instance to show model definitions T6SSii and T6SSiii in TXSS+/bacterial subpackage:

msl_data definition TXSS+/bacterial T6SSii T6SSiii

To show all models definitions in TXSS+/bacterial subpackage:

msl_data definition TXSS+/bacterial

To create a skeleton for your own model package (to access init subcommand check modeler instaltion):

msl_data init --pack-name <MY_PACK_NAME> --maintainer <"mantainer name"> --email <maintainer email> --authors <"author1, author2, ..">

above msl_data with required options. Below I add option but recommended options.

msl_data init --pack-name <MY_PACK_NAME> --maintainer <mantainer name> --email <maintainer email> --authors <"author1, author2, .."> \
--license cc-by-nc-sa --holders <"the copyright holders"> --desc <"one line package description">

To list all msl_data subcommands:

msl_data --help

To list all available options for a subcommand:

msl_data <subcommand> --help

For models not stored in macsy-models the commands available, search, installation from remote or upgrade from remote are NOT available.

For models NOT stored in macsy-models, you have to manage them semi-manually. Download the archive (do not unarchive it), then use msl_data to install the archive.