macOS#

Install via Conda#

Warning

At this time, we do not provide a conda package for our GUI tools. This means if you want to install e.g., TOPPView or SwathWizard for use in for example one of our tutorials, please refer to a different installation method below.

You can use conda or mamba 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 or mamba. In the following, every mention of conda may be substituted by mamba for faster environment solving.

  2. We recommend to create a new environment with one of the supported python version versions:

     conda create -n openms python=3.10

  3. Add some channels to find dependencies:

     conda config --add channels defaults
 conda config --add channels bioconda
 conda config --add channels conda-forge

    Note

    You can also add the channels for your current environment only with the --env option.

    Warning

    The order of the channels is important!

    Note

    conda-forge might already be added if you are using Mambaforge.

  4. 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 package is required to use the adapters in the openms package.

    Warning

    Due to unavailability of a large part of the thirdparty tools for macOS via conda, we are not providing a openms-thirdparty package on macOS either.

    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 macOS installer#

To install OpenMS on macOS, run the following steps:

  1. Download and install the macOS drag-and-drop installer from the archive.

  2. Double click on the downloaded file. It will start to open the OpenMS-<version>-macOS.dmg disk image file.

Opening OpenMS-<version>-macOS.dmg

  1. Verify the download.

Verifying OpenMS-<version>-macOS.dmg

  1. Agree to the license agreements.

License agreement

  1. Drag OpenMS to the Applications folder.

Move to Applications

  1. It will start copying to applications.

Preparing to copy to Applications Copying to Applications

To use TOPP as regular app in the shell, add the following lines to the ~/.profile file.

Warning

Known Installer Issues

  1. Nothing happens when you click OpenMS apps or the validity of the developer could not be confirmed.

    This usually means the OpenMS software lands in quarantine after installation of the .dmg. Since macOS Catalina (maybe also Mojave) all apps and executables have to be officially notarized by Apple but we currently do not have the resources for a streamlined notarization workflow.

    To have a streamlined experience without blocking popups, it is recommended to remove the quarantine flag manually, using the following steps:

    Open the Terminal.app and type the following (replace the first line with the actual installation directory):

    cd /Applications/OpenMS-<version>
sudo xattr -r -d com.apple.quarantine *

  2. Bug with running Java based thirdparty tools like MSGFPlusAdapter and LuciphorAdapter from within TOPPAS.app

    If you face issues while running Java based thirdparty tools from within TOPPAS.app, run the TOPPAS.app from within the Terminal.app (e.g. with the open command) to get access to the path where Java is located. Java is usually present in the PATH of the terminal. Advanced users can set this path in the Info.plist of/inside the TOPPAS.app.

    export OPENMS_TOPP_PATH=<OpenMS-PATH>
source ${OPENMS_TOPP_PATH}/.TOPP_bash_profile

    Make sure <OpenMS-PATH> points to the folder where OpenMS is installed locally (e.g., /Applications/OpenMS-<version>)

Run OpenMS inside a (Bio)Container#

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

  2. Pull an image from one of the following registries:

  • OpenMS GitHub Container Registry for nightly binaries AND releases:

    On our registry, we provide one image for the library (with contrib) and one for the executables (with thirdparty).

    1. openms-library

    2. openms-executables

    They can be pulled/run via the following commands:

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

    singularity run ghcr.io/openms/openms-library-sif
singularity run ghcr.io/openms/openms-executables-sif

    Note

    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:3.1.0 to receive a stable version.

  • Otherwise, the BioContainers Registries and the associated Galaxy project provide native containers based on 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

Note

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 macOS.