How to install emzed?¶

You can install emzed using pip:

pip install emzed

We also highly recommend using a virtual environment for setting up emzed.

Installation on Windows¶

For a simplified setup on Windows we recommend the emzed-spyder Windows installer which ships with all dependencies. You can find the instructions at https://emzed.ethz.ch/get_started.html.

Installation on Linux¶

pyopenms depends on 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.

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This message is slightly outdated, the shared library names start with an underscore, so it should read _pyopenms*.so.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