GNU/Linux#

Install via Conda#

You can use conda to install the OpenMS library and tools without user interface. Depending on the conda channel, you can obtain release versions (bioconda channel) and nightly versions (openms channel).

  1. Follow the instructions to install conda.

  2. Add channels for dependencies:

     conda config --add channels defaults
     conda config --add channels bioconda
     conda config --add channels conda-forge
    
  3. Install any of the following packages related to OpenMS

openms contains all OpenMS C++ command-line tools. GUI applications like TOPPView currently cannot be installed via conda.

libopenms is the C++ library required for the OpenMS C++ Tools to work. This is also an auto-installed dependency of openms.

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.

via bioconda for release versions

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

or our own openms channel for nightly snapshots (which are build based on the same bioconda dependencies)

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

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.

Install via the provided 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 step 1

    Make sure you source the provided environment file using: source /opt/qt59/bin/qt59-env.sh

  5. Adapters are not finding thirdparty applications

    Executables for thirdparty applications can be found in: /usr/share/OpenMS/THIRDPARTY Add the folders in your PATH for a convenient use of the adapters.

Run via a (Bio)Container#

Install a containerization software (e.g., Docker or Singularity)

Our container support is constantly updated. Docker images provided by us can be obtained via ghcr.io.

  1. openms-library

  2. openms-executables

Docker images from our own continuous integration can be installed via the following commands:

docker pull ghcr.io/openms/openms-library
docker pull ghcr.io/openms/openms-executables

per default this results in the download of the latest nightly snapshot. Specify a release version (e.g., docker pull ghcr.io/openms/openms-library:2.7.0 to receive a stable version.

Otherwise, the BioContainers Registries and the associated Galaxy project provide native containers from our bioconda packages for both Docker and Singularity.

  1. BioContainers libopenms

  2. BioContainers openms

  3. BioContainers openms-thirdparty

  4. BioContainers pyOpenMS

Images of the containers can be pulled via or one of the following commands:

docker pull quay.io/biocontainers/libopenms
docker pull quay.io/biocontainers/openms
docker pull quay.io/biocontainers/pyopenms
docker pull quay.io/biocontainers/openms-thirdparty
singularity run https://depot.galaxyproject.org/singularity/libopenms
singularity run https://depot.galaxyproject.org/singularity/openms
singularity run https://depot.galaxyproject.org/singularity/pyopenms
singularity run https://depot.galaxyproject.org/singularity/openms-thirdparty

If Singularity images fail to download or run, try to use the Docker images as Singularity will automatically convert them.

Dockerfiles to build different kind of images (e.g., for ArchLinux) yourself can be found on GitHub in our OpenMS/dockerfiles repository. They usually follow our build instructions closely, so you can have a look on how this is done in a clean environment.

Build OpenMS from source#

To build OpenMS from source, follow the build instructions for Linux.