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 (
Follow the instructions to install conda.
Add channels for dependencies:
conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge
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.
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.
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.
Some thirdparty software used via adapter tools in OpenMS might also require an installed JavaVM.
Install via the provided Debian package#
sudo apt-get install gdebi sudo gdebi /PATH/TO/OpenMS.deb
If you encounter errors with unavailable packages, troubleshoot using the following steps.
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.
ICU with its
You can find the missing version on pkgs.org and install it with
gdebi, too. You can have multiple versions of ICU installed.
Error while executing a tool
To ensure the tool functionality, make sure you add the
OPENMS_DATA_PATHvariable to your environment as follow
Thirdparty installation of Qt5 in step 1
Make sure you source the provided environment file using:
Adapters are not finding thirdparty applications
Executables for thirdparty applications can be found in:
/usr/share/OpenMS/THIRDPARTYAdd the folders in your
PATHfor a convenient use of the adapters.
Run via a (Bio)Container#
Our container support is constantly updated. Docker images provided by us can be obtained via ghcr.io.
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.
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.