GNU/Linux#

Install via Conda#

Use conda or bioconda to install OpenMS.

  1. Follow the instructions to install conda.

  2. Install OpenMS using conda: conda install -c openms openms

  3. Other OpenMS packages can be installed using:

    conda install -c openms pyopenms
conda install -c openms openms-thirdparty
conda install -c openms libopenms

openms contains OpenMS C++ Tools.

libopenms is the C++ library required for the OpenMS C++ Tools to work.

pyopenms is the python package that allows to use algorithms from libopenms in Python.

openms-thirdparty are external tools that are wrapped in OpenMS with adapters. This is required to use the adapters in the openms package.

To install using bioconda:

conda install -c bioconda openms
conda install -c bioconda libopenms
conda install -c bioconda openms-thirdparty

Install via Debian package#

For Debian-based Linux users, it is suggested to use the deb-package provided. It is most easily installed with gdebi which automatically resolves the dependencies available in the PPA Repositories.

sudo apt-get install gdebi
sudo gdebi /PATH/TO/OpenMS.deb

If you encounter errors with unavailable packages, troubleshoot using the following steps.

  1. Qt5 (or one of its packages, e.g. qt5xbase) is missing. It might be because your Debian is too old to have a recent enough version in its official repositories. It is suggested to use the same packages that are used while building (make sure to adapt the Qt version and your Debian/Ubuntu version, here Xenial):

    sudo add-apt-repository ppa:beineri/opt-qt59-xenial
sudo apt-get update

    Run the installation again.

  2. ICU with its libicu is missing. You can find the missing version on pkgs.org and install it with gdebi, too. You can have multiple versions of ICU installed.

  3. Error while executing a tool To ensure the tool functionality, make sure you add the OPENMS_DATA_PATH variable to your environment as follow export OPENMS_DATA_PATH=/usr/share/OpenMS

  4. Thirdparty installation of Qt5 in 1 Make sure you source the provided environment file using: source /opt/qt59/bin/qt59-env.sh

    Executables for THIRDPARTY applications can be found in: /usr/share/OpenMS/THIRDPARTY

  5. Add the folders in your PATH for a convenient use of the adapters.

Install via package managers#

Packaged versions of OpenMS are provided for Fedora, OpenSUSE, Debian, and Ubuntu. You can find them to download here. For other GNU/Linux distributions or to obtain the most recent version of the library, installation should be done via building from the source code.

Important

These packages are not directly maintained by the OpenMS team and they can not be guaranteed to have the same behaviour as when building it from source code. Also, their availability and version is subject to change and support might be limited (due to unforeseen or untested behaviour). It is suggested not to install them parallel to our Debian package.

Note

Some thirdparty software used via adapter tools in OpenMS might also require an installed JavaVM.

Run via a (Bio)Docker image#

Make sure you have Docker installed.

Our Docker support is constantly updated. Images can be obtained via ghcr.io.

  1. openms-executables

  2. openms-library

Or via BioContainers Registeries.

  1. BioContainers libopenms

  2. BioContainers openms

  3. BioContainers openms-thirdparty

  4. BioContainers pyOpenMS

Docker images can be pulled via or one of the following commands:

docker pull biocontainers/openms
docker pull openms/library
docker pull openms/executables
docker pull openms/pyopenms