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 Installation procedure

To develop new models and share them, MacSyLib requires git and the python library GitPython

Below the procedure to install MacSyLib in modeler mode in a virtualenv

python3 -m venv macsylib
cd macsylib
source bin/activate
python3 -m pip install macsylib[model]

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

Warning

But you have to install git by yourself (using your preferred package manager)

From Conda/Mamba

MacSylib is packaged for Conda/Mamba. The Conda/Mamba package include modeler dependencies

From container

From version 2.0 and above, a docker image is available. This image allow you to develop models.

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 git repository with a skeleton for your own model package:

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 optional 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.