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. We also provide container so you can use macsyfinder directly.
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 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).
MacSyFinder Installation procedure
It is recommended to use pip to install the MacSyFinder package.
Archive overview
doc => the documentation in html and pdf
test => all what is needed for unitary tests
macsypy => the macsyfinder python library
setup.py => the installation script
setup.cfg => the installation script
pyproject.toml => the project installation build tool
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.
python3 -m pip install 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
python3 -m pip install --user macsyfinder
installation in a virtualenv
python3 -m venv macsyfinder
cd macsyfinder
source bin/activate
python3 -m pip install 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 -m venv macsyfinder
To delete it, remove the directory
rm -R macsyfinder
From Conda/Mamba
From version 2.0, MacSyFinder is packaged for Conda/Mamba
mamba install -c macsyfinder=x.x
Where x.x is the macsyfinder version you want to install
From container
With Docker
The docker image is available on Docker Hub (https://hub.docker.com/repository/docker/gempasteur/macsyfinder) The computations are performed under msf user in /home/msf inside the container. So You have to mount a directory from the host in the container to exchange data (inputs data, and results) from the host and the container. The shared directory must be writable by the msf user or overwrite the user in the container by your id (see example below)
Furthermore the models are no longer packaged along macsyfinder. So you have to install them by yourself. For that we provide a command line tool macsydata which is inspired by pip.
macsydata search PACKNAME
macsydata install PACKNAME== or >=, or ... VERSION
To work with Docker you have to install models in a directory which will be mounted in the image at run time
mkdir shared_dir
cd shared_dir
install desired models in my_models directory
docker run -v ${PWD}/:/home/msf -u $(id -u ${USER}):$(id -g ${USER}) gempasteur/macsyfinder:<tag> macsydata install --target /home/msf/my_models <MODELS_PACK>
run msf against all models contains in <MODELS_PACK>
docker run -v ${PWD}/:/home/msf -u $(id -u ${USER}):$(id -g ${USER}) gempasteur/macsyfinder:<tag> macsyfinder --db-type unordered_replicon --models-dir=/home/msf/my_models/ --models <MODELS_PACK> all --sequence-db my_genome.fasta -w 12
With Apptainer (formely Singularity)
As the docker image is registered in docker hub you can also use it directly with Apptainer (https://apptainer.org/). Unlike docker you have not to worry about shared directory, your HOME and /tmp are automatically shared.
# install desired models in my_models directory
apptainer run -H ${HOME} docker://gempasteur/macsyfinder:<tag> macsydata install --target my_models <MODELS_PACK>
# run msf against all models contains in <MODELS_PACK>
apptainer run -H ${HOME} docker://gempasteur/macsyfinder:<tag> macsyfinder --db-type unordered_replicon --models-dir=my_models --models <MODELS_PACK> all --sequence-db my_genome.fasta -w 12
If you intend to run apptainer from host which cannot access internet (cluster node for instance), you have to
download the image locally
transfert the image file on the right file system
and then use it.
apptainer build msf-<tag>.simg docker://gempasteur/macsyfinder:<tag>
cp msf-<tag>.simg <cluster_file_system>
apptainer run -H ${HOME} msf-<tag>.simg macsyfinder --db-type unordered_replicon --models-dir=my_models --models <MODELS_PACK> all --sequence-db my_genome.fasta -w 12
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 (https://github.com/macsy-models) or locally installed. The general syntax for macsydata is:
macsydata <general options> <subcommand> <sub command options> <arguments>
To list all models available on macsy-models:
macsydata available
To search for models on macsy-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
To install it in your home (./macsyfinder/data):
macsydata install --user <model name>
To install it in any directory:
macsydata install --target <model dir> <model_name>
To know how to cite a model package:
macsydata cite <model name>
To show the model definition:
macsydata definition <package or subpackage> model1 [model2, ...]
for instance to show model definitions T6SSii and T6SSiii in TXSS+/bacterial subpackage:
macsydata definition TXSS+/bacterial T6SSii T6SSiii
To show all models definitions in TXSS+/bacterial subpackage:
macsydata definition TXSS+/bacterial
To create a skeleton for your own model package:
macsydata init --pack-name <MY_PACK_NAME> --maintainer <mantainer name> --email <maintainer email> --authors <"author1, author2, ..">
above macsydata with required options. Below I add optioanl but recommended options.
macsydata 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 macsydata subcommands:
macsydata --help
To list all available options for a subcommand:
macsydata <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 macsydata to install the archive.
