Run MetFrag in batch mode in a container.
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README.md
metfrag-cli-batch.xml
test_cmds.txt

README.md

Metfrag-CLI-Batch

Version: 0.1

Short Description

Run MetFrag in batch mode in a container.

Description

MetFrag is a freely available software for the annotation of high precision tandem mass spectra of metabolites which is a first and critical step for the identification of a molecule's structure. Candidate molecules of different databases are fragmented in silico and matched against mass to charge values. A score calculated using the fragment peak matches gives hints to the quality of the candidate spectrum assignment. The Metfrag-CLI-Batch container gets either a file or folder containing parameter inputs for MetFrag-CLI (https://github.com/c-ruttkies/MetFragRelaunched) to process them in batch mode.

Key features

  • Annotation of fragments

Functionality

  • Annotation / MS

Approaches

  • Metabolomics

Instrument Data Types

  • LC-MS/MS

Tool Authors

  • Christoph Ruttkies (IPB-Halle)

Container Contributors

Git Repository

Installation

docker build -t metfrag-cli-batch .

Usage Instructions

For direct docker usage:

docker run -v /data:/data metfrag-cli-batch InputFile=/data/parameters.txt