OpenMS

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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

BSD/3­clause

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

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