openms/dockerfiles

This repository holds Dockerfiles for creating docker images for several OpenMS configurations based on different base images.

OpenMS

OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software. OpenMS is free software available under the three clause BSD license and runs under Windows, macOS, and Linux.

It comes with a vast variety of pre-built and ready-to-use tools for proteomics and metabolomics data analysis (TOPPTools) as well as powerful 1D, 2D and 3D visualization (TOPPView).

OpenMS offers analyses for various quantitation protocols, including label-free quantitation, SILAC, iTRAQ, TMT, SRM, SWATH, etc.

It provides built-in algorithms for de-novo identification and database search, as well as adapters to other state-of-the art tools like X!Tandem, Mascot, Comet, etc. It supports easy integration of OpenMS built tools into workflow engines like KNIME, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept and a unified parameter handling via a 'common tool description' (CTD) scheme.

With pyOpenMS, OpenMS offers Python bindings to a large part of the OpenMS API to enable rapid algorithm development. OpenMS supports the Proteomics Standard Initiative (PSI) formats for MS data. The main contributors of OpenMS are currently the Eberhard-Karls-Universität in Tübingen, the Freie Universität Berlin, and the ETH Zürich.

Features

• Core C++ library under three-clause BSD licence using modern C++17
• Python bindings to the C++ API through pyOpenMS
• Major community file formats supported (mzML, mzXML, mzIdentXML, pepXML, mzTab, etc.)
• Over 150+ individual analysis tools (TOPP Tools), covering most MS and LC-MS data processing and mining tasks
• Powerful 1D, 2D and 3D visualization tools (TOPPView)
• Support for most MS identification and quantification workflows (targeted, DIA, label-free, isobaric and stable isotope)
• Support for all major platforms (Windows [XP, 7, 8, 10], macOS and Linux)

Documentation

Users and developers should start by reading the OpenMS documentation. OpenMS API reference documentation and advanced developer doxygen documentation can be browsed here.

openms.readthedocs.io documentation aims at being an entry point for users and developers alike. It is trying to be mostly version-independent and therefore only consists of one main branch. We may introduce tags for older releases in the future.

The OpenMS API reference has several endpoints:

1. nightly: OpenMS API reference and advanced developer documentation of nightly releases.
2. release/latest : OpenMS API reference and advanced developer documentation of latest stable release.
3. release/${version} : OpenMS API reference and advanced developer documentation of an older version.

Documentation for the Python bindings pyOpenMS can be found on the pyOpenMS online documentation.

Citation

Please cite:

Pfeuffer, J., Bielow, C., Wein, S. et al. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data, Nat Methods 21, 365–367 (2024). https://doi.org/10.1038/s41592-024-02197-7

The file AUTHORS contains a list of all authors who worked on OpenMS.

Licence

OpenMS is released under the three clause BSD licence.

dockerfiles's Issues

dockerfiles miss debian docker image pecularities (DEBIAN_FRONTEND)

e.g. while processing of apt-get during the build:

debconf: unable to initialize frontend: Dialog
debconf: (TERM is not set, so the dialog frontend is not usable.)
debconf: falling back to frontend: Readline
debconf: unable to initialize frontend: Readline
debconf: (This frontend requires a controlling tty.)
debconf: falling back to frontend: Teletype
dpkg-preconfigure: unable to re-open stdin: 

add labels to help organize images by project

because best practices and to be courteous to BioContainers project

move to OpenMS/OpenMS repo

providing a complete contrib from-source-build

are there any any up- or down-sides to that. Can we briefly discus that here?

Integrate into OpenMS repository?

@mwalzer @hroest @timosachsenberg @lukaszimmermann
I would like to hear opinions on integrating the dockerfiles into the OpenMS repository.
I think that is how the Dockerhub triggers are supposed to work. Whenever there is a change in the repo (on whitelisted branches, e.g. nightly, release*, qt5) it will use the dockerfiles in there to build it.
We don't have to care about maintaining folders for different branches, and have better tagging support for the dockerhub builds.

Cleanup!!

• remove all qt4 images
• remove all Travis images
• remove biocontainers (should be done from bioconda automatically)
• remove special trigger variables only used for dockercloud
• update metadata
• update base images
• update software
• evaluate Users and entry points
• evaluate branching, tags and deployment strategy