Your current Windows Installation is broken ??? Goto emzed does not start up (anymore) !!!.

The current version of emzed was developed and tested on 32 and 64 bit Windows XP, 7 and 8 as well as 64 bit Ubuntu Linux and Mac OS X. The current version of emzed relies on Python 2.7.X and is not Python 3 ready.


If you have problems installing emzed, please use the discussion group at

Installation on 64 bit Windows


For installing emzed on Windows please follow the stepwise instructions carefully. Version numbers and file names matter.

  1. Download and install Microsoft Visual C++ 2008 SP1 Redistributable Package (x64) from

  2. Download WinPython version (no other version !!!) for 64 bit from


    Do not confuse WinPython with the official Python for windows release from

    Take care to install the 64 bit version.

  3. Run the WinPython installer. This step only unpacks WinPython to a target directory you can choose. We recommend to use C:\WinPython- unless you have some special reasons.


    Keep the install target in mind, you will need this path for the next step.

  4. Download the installer and run it with administator rights.

    The installer asks for the path to the Python interpreter to use.

    If you folllowed the recommandation from step 3, the path to the Python interpreter is C:\WinPython-\python-2.7.9.amd64\python.exe. Else you will find the python.exe inside the python-2.7.9.amd64 subfolder of the installation target from the previous step.

    The installation process opens a terminal window and runs for a few minutes, so stay patient.

  1. Now you should find emzed in your Windows start menu.
  2. optional: install R if you want to use XCMS or any other R library.
  3. In case of problems, read emzed does not start up (anymore) !!!.

Installation on Ubuntu Linux

The following package names are for Ubuntu 14.04 LTS**, for other distributions the names may sligthly differ (for example python2.7-matplotlib instead of python-matplotlib). If needed you can eg use $ apt-cache search matplotlib to lookup exact names on your machine.

  1. First, you should install numpy, scipy and matplotlib globally as they are difficult to build. PyQt4 should be installed globally too:

    $ sudo apt-get install python2.7
    $ sudo apt-get install python-numpy python-scipy python-matplotlib python-qt4
    $ sudo apt-get install python-pandas python-scikits-learn
    $ sudo apt-get install libncurses-dev
    $ sudo apt-get install python-qwt5-qt4
    $ sudo apt-get install python-virtualenv
  2. For the final installation download the installation script from The script will ask for the target folder, we recommend to use the proposed default value.:

    $ bash
  3. After successful installation the script prints the direct path for starting emzed from the command line. Further, you should find the emzed icon on your desktop.

  4. optional: install R if you want to use XCMS or any other R library:

    $ sudo apt-get install r-base

Manual Installation on Linux

If you have a Linux distribution for which the previous instructions failed, you can install emzed manually as described now:

  1. Install Python 2.7.

  2. Install numpy, at least version 1.7.0.

  3. Install Python packages scipy, matplotlib, PyQt4 and virtualenv.

  4. We recommend to install emzed using virtualenv as described below.


    virtualenv is a Python tool to create virtual environments which keep your Python installation in a clean and consistent state. virtualenv creates a local Python installation in a given folder without version conflicts to parallell installations and avoids cluttering your system.

    Execute the listed statements, they will install emzed inside the folder emzed2 in your home directory:

    $ cd
    $ virtualenv-2.7 --system-site-packages emzed2
    $ cd emzed2
    $ source bin/activate
    (emzed2)$ easy_install pyopenms==2.0
    (emzed2)$ pip install cython
    (emzed2)$ pip install "guiqwt<2.4.0" --allow-external guiqwt --allow-unverified guiqwt
    (emzed2)$ pip install "guidata<1.7.0" --allow-external guidata --allow-unverified guidata
    (emzed2)$ pip install sphinx
    (emzed2)$ easy_innstall ipython==0.10
    (emzed2)$ pip install
    (emzed2)$ deactivate

    Now you should be able to start emzed workbench:

    $ source ~/emzed2/bin/activate
    $ emzed.workbench
  1. optional: install R if you want to use XCMS or any other R library.

Manual Installation on Mac OS X

To get emzed with pyqt and pyqwt running on Mac OS X, we need to install it with brew, the missing package manager for OS X.

  1. If you’re running ruby for the first time, you maybe need to agree to the Xcode license:

    $ sudo xcodebuild -license
  2. Install brew:

    $ /usr/bin/ruby -e "$(curl -fsSL"
    $ brew update
    $ brew tap homebrew/science
  3. Install Python 2.7:

    $ brew install python
    $ brew linkapps python
    $ brew link python
    $ brew install hdf5
  4. Install virtualenv, create a Virtual Environment for emzed and activate it:

    $ /usr/local/bin/python2.7 -m pip install --upgrade pip
    $ /usr/local/bin/python2.7 -m pip install matplotlib
    $ /usr/local/bin/python2.7 -m pip install virtualenv
    $ /usr/local/bin/python2.7 -m virtualenv --system-site-packages emzed
    $ cd emzed/
    $ echo 'import site; site.addsitedir("/usr/local/lib/python2.7/site-packages")' >> lib/python2.7/site-packages/homebrew.pth
    $ . bin/activate
  5. Install the necessary packages using brew and pip:

    $ brew install pyqt
    $ brew install pyqwt
    $ pip install pyopenms==2.0
    $ pip install ipython==0.10
    $ pip install numpy
    $ pip install scipy
    $ pip install tables
    $ pip install cython
    $ pip install "guidata<1.7.0" --allow-external guidata --allow-unverified guidata
    $ pip install "guiqwt<2.4.0" --allow-external guiqwt --allow-unverified guiqwt
    $ pip install sphinx
    $ easy_install
    $ pip install
  6. add workaround for matplotlib in virtualenv

Workaround taken from Add the following lines in your ~/.bash_profile:

function frameworkpython {
    if [[ ! -z "$VIRTUAL_ENV" ]]; then
        PYTHONHOME=$VIRTUAL_ENV /usr/local/bin/python "$@"
        /usr/local/bin/python "$@"

install the frameworkpython function: source ~/.bash_profile

Getting the latest development version of emzed

emzed is hosted on, after installing git you can check out the latest version using:

git clone git://