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How to get started

Installation of eMZed as part of Spyder

The easiest way to get started is to install emzed as part of the Spyder IDE. For that purpose, we provide emzed-spyder, which installs emzed and emzed-gui during first startup and adds support for workflow development.

Installation on Windows

For Windows, use the latest setup_emzed_spyder_3.X.Y.exe from our releases.

Before the installer can be run, you have to change the file permissions

Right click on the file in the explorer to edit the properties:

Benefits of this installer
  • The installer also installs a separate Python interpreter for the user to avoid interference with other Python installations on the system or to avoid Administrator privileges.
  • Installs runtime dlls which are sometimes missing or not aligned with the details of the current Windows installation.
  • The installer registers emzed-spyder as a Windows application including icons so you can start emzed-spyder directly from the Windows desktop.
  • Enables clean deinstallation.

Installation on Linux

emzed depends on pyopenms, which in turn requires shared libraries that may not be present by default on Linux systems and therefore need to be installed manually. If you're on a recent Debian-based distribution, run sudo apt-get install libglib2.0-0 to install the required dependency.

If this is not enough

When importing emzed, a typical error message pointing to missing shared libraries is:

pyopenms: ======================================================================
pyopenms: Error when loading pyOpenMS libraries!
pyopenms: Libraries could not be found / could not be loaded.
pyopenms:
pyopenms: To debug this error, please run ldd (on linux), otool -L (on macOS) or dependency walker (on windows) on
pyopenms:
pyopenms: /.venv/share/pyopenms_venv/lib/python3.12/site-packages/pyopenms/pyopenms*.so
pyopenms:
pyopenms: ======================================================================

This message is slightly outdated, the shared library names start with an underscore, so it should read _pyopenms*.so.

Running the command (with an adapted path)

ldd /.venv/share/pyopenms_venv/lib/python3.12/site-packages/pyopenms/_pyopenms*.so | grep 'not found'

will list the missing dependencies.

Installation with pip

For all operating systems, emzed-spyder can also be installed with:

pip install emzed-spyder

Use a virtual environment when installing with pip. Supported Python versions are 3.11 through 3.13.

During the first start-up emzed-spyder will install all other emzed core packages for you.

Install the core packages manually

If you do not need the Spyder IDE, install the core packages directly:

pip install emzed emzed-gui

About the core packages