OpenMS
Description
OpenMS is a versatile open-source library for mass spectrometry data analysis. Based on this library, we offer a collection of command-line tools ready to be used by end users.
OpenMS: The name of our library, which contains the algorithms. You cannot use this directly, unless you are a programmer.
TOPPView: View and explore LC-MS data, alignments, groups, peptide identifications and more!
TOPPAS: A graphical workflow design tool, which allows to create pipelines from all TOPP tools (and UTILS).
TOPP tools: A set of command line tools, each of which is a building block of an analysis pipeline. These tools chained together in a way that fits the requirements of the user. Accessible from a command prompt/shell or via TOPPAS. See also: TOPP tutorial and TOPP documentation
UTILS: Similar to TOPP tools, but with more supporting character, which you'd rarely use in a productive pipeline - but rather during pipeline construction or parameter optimization. See also: [UTILS documentation UTILS documentation]
License
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of openms and load default version of openms as
module avail openms/ # list available modules module load openms # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail openms
and choose explicit version you want to use.
Graphic tools
jenicek$ ssh skirit.metacentrum.cz skirit$ qsub -I -l select=1:ncpus=2:mem=4gb:scratch_local=1gb -l walltime=1:00:00 took11$ module add gui took11$ gui start
In remote desktop
TOPPView file1.mzML
Notice: This application use or needs GUI – graphical interface. To use the application in graphical mode see Remote desktop or X-Window.
Singularity docker image
Tutorial for singularity is here
Documentation
http://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/index.html
Homepage
URL: http://www.openms.de