Installation

MacSyFinder works with models for macromolecular systems that are not shipped with it, you have to install them separately. See the msf_data section below. We also provide container so you can use macsyfinder directly.

MacSyFinder Installation procedure

To develop new models and share them, MacSyFinder requires git and the python librarie GitPython

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

python3 -m venv macsyfinder
cd macsyfinder
source bin/activate
python3 -m pip install macsyfinder[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

From version 2.0 and above, MacSyFinder 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 msf_data

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

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

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

To list all models available on macsy-models:

msf_data available

To search for models on macsy-models:

msf_data search TXSS

you can also search in models description:

msf_data search -S secretion

To install a model package:

msf_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 (./macsyfinder/data):

msf_data install --user <model name>

To install it in any directory:

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

To know how to cite a model package:

msf_data cite <model name>

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

msf_data show <model package name>

for instance msf_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:

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

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

msf_data definition TXSS+/bacterial T6SSii T6SSiii

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

msf_data definition TXSS+/bacterial

To create a git repository with a skeleton for your own model package:

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

above msf_data with required options. Below I add optioanl but recommended options.

msf_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 msf_data subcommands:

msf_data --help

To list all available options for a subcommand:

msf_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 msf_data to install the archive.