The Workflow4Metabolomics, W4M in short, is a French infrastructure offering software tool processing, analyzing and annotating metabolomics data. It is based on the Galaxy platform.
MS-based metabolomics data processing and compound annotation pipeline.
Author: Ron Wehrens [aut, cre] (author of GC-MS part), Pietro Franceschi [aut] (author of LC-MS part), Nir Shahaf [ctb], Matthias Scholz [ctb], Georg Weingart [ctb] (development of GC-MS approach), Elisabete Carvalho [ctb] (testing and feedback of GC-MS pipeline)
Maintainer: Ron Wehrens <ron.wehrens at gmail.com>
Citation (from within R, enter citation("metaMS")):
Wehrens R, Weingart G and Mattivi F (2014). “metaMS: An open-source pipeline for GC-MS-based untargeted metabolomics.” J. Chrom. B, 966, pp. 109-116.
Homepage: https://github.com/Bioconductor-mirror/metaMS/
Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.
Homepage: https://galaxyproject.org/
Conda is package manager that among many other things can be used to manage Python packages.
#To install miniconda2
#http://conda.pydata.org/miniconda.html
#To install the metaMS R library using conda:
conda install bioconductor-metams bioconductor-xcms r-batch
#To set an environment:
conda create -n bioconductor-metams bioconductor-metams bioconductor-xcms r-batch
#To activate the environment:
. activate bioconductor-metams
Test and Deploy with Confidence. Easily sync your GitHub projects with Travis CI and you'll be testing your code in minutes!
Planemo test using conda: passed
- Yann Guitton @yguitton - LABERCA - Laboratory of Food Contaminants and Residue Analysis - Ecole Nationale Vétérinaire, Agroalimentaire et de l'Alimentation Nantes-Atlantique - France
- Gildas Le Corguillé @lecorguille - ABiMS / IFB - UPMC/CNRS - Station Biologique de Roscoff - France