Installation

The Project contains two main parts:

  1. The mzbsuite package;

  2. The scripts and workflow files making use of its functions.

The mzbsuite folder (in Python this is called a package) contains higher-level functions that can be imported from other scripts and used to create complex processing pipelines, while the scripts and workflow folders contain files that make use of functions implemented in mzbsuite to run single modules or the processing pipeline as a whole.

The file environment.yml contains all the minimal dependencies for the project, and should install the functions in mzbsuite as well. However, if this does not work, the mzbsuite package can be installed separately using the setup.py file in the mzbsuite folder, via pip (see here)

Docker container

For less experienced users, we recommend installing via Docker. You can find instructions on how to install the Docker Engine here: https://docs.docker.com/get-docker/

Once the Docker Engine has been correctly installed, you can download the project’s Docker image from:

and launch it from the Graphical User Interface (GUI) of Docker.

This should open a terminal within the Docker environment where you can start using the project’s modules immediately!

Manual install

If you prefer to install the project directly in your local environment or just want to use the functions in your own scripts, you can download the project’s repository. The project is currently hosted on the Swiss Data Science Center GitLab server, you can find the repository here:

To download the project, you simply need to clone it into a location of your choice:

git clone git@renkulab.io:biodetect/mzb-workflow.git

If you don’t have Git installed, you can follow instructions here. We recommend using Git because it allows to easily update the package and tracking any changes you make.

This will create a folder called mzb-workflow in the current working directory.

Hint

If you don’t want to use Git, you can directly download an archive of the repository from GitLab and extract it manually.

You can then install the necessary packages using the conda package manager and the environment.yml file:

cd mzb-workflow    # chdir mzb-workflow in Windows
conda env create -f environment.yml

Hint

If you don’t have Anaconda installed, you can can get the installer from https://www.anaconda.com/download.

This should install the mzbsuite package as well, but if this does not work, you can simply install it via pip as:

pip install -e .

the -e flag will install the package in editable mode, so that you can make changes to the functions in mzbsuite and they will be reflected in your environment.

You can check whether mzbsuite has been installed by running:

conda list -n mzbsuite

and check that mzbsuite appears in the list.

If there are no errors then you’re all set up and can start using the modules.