Docker RStudio Container for Metabolomics Data Processing

This is a customised flavor of https://github.com/hexylena/docker-rstudio-notebook for Metabolomics Data Processing with R packages. Most of the code was taken from Data Integration Hackathon analyses.

Additionnal Metabolomics R packages are from RforMasspectrometry web site

• factoextra
• msdata
• mzR
• r hdf5
• lgatto/rpx
• MsCoreUtils
• QFeatures
• Spectra
• ProtGenerics
• PSMatch
• pheatmap
• limma
• MSnID
• RforMassSpectrometry/SpectraVis

##Addition of other packages

• metaMS
• msPurity
• SpectraQL

Specific Data Integration R packages are pre-installed from Data Integration Hackathon:

• MixOmics (v6.22 Bioconductor - mixOmics)
• iClusterPlus (v1.34 Bioconductor - iClusterPlus)
• MOFA2 (v1.8 Bioconductor - MOFA2)

Other pre-installed R packages:

• tidyverse (v1.3.2 CRAN - tidyverse)
• tidymodels (CRAN - tidymodels)
• targets (v0.14.1 GitHub - targets)

Other pre-installed linux system package:

• quarto (v1.2.269 Quarto - get started)

This image can be used as a Galaxy Interactive Tool.

Installing it as a Galaxy Interactive Tool on a Galaxy instance

First make sure your Galaxy instance is configured to support Interactive Tools.

Then you need to copy the ./interactivetool_rstudio_metabolomics-dataprocessing.xml file into $GALAXY_ROOT/tools/interactive/.

Add this new tool to $GALAXY_ROOT/config/tool_conf.xml:

<?xml version='1.0' encoding='utf-8'?>
<toolbox monitor="true">
  [...]
  <section id="interactive_tools" name="Interactive tools">
    [...]
    <tool file="interactive/interactivetool_rstudio_metabolomics-dataprocessing.xml" />
  </section>
</toolbox>

And add this tool to $GALAXY_ROOT/config/job_conf.xml: follow the instructions in the Interactive Tools tutorial, and adapt depending on your setup.