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workflow4metabolomics / metaMS

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gcms metabolo workflow4metabolomics

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metaMS for Galaxy

install with bioconda Build Status

Our project

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.

metaMS

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

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

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/

Dependencies using Conda

install with bioconda

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

Travis

Build Status

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Test Status

Planemo test using conda: passed

Historic contributors