Command line tool installation and configuration

command-line-tool-installation-and-configuration

Summary

Installation and configuration of MetaboDirect and its dependencies (Python, R, Cytoscape, and domain libraries) to establish a working command-line environment for FT-ICR MS data analysis. This skill ensures all required computational infrastructure is in place before running the pipeline.

When to use

Before launching any MetaboDirect pipeline run on a new system or environment. Trigger conditions: (1) first-time setup on a target OS (Windows, Linux, or macOS); (2) environment lacks Python 3.5+, R 4.0+, or Cytoscape 3.8+; (3) required Python packages (numpy, pandas, seaborn, py4cytoscape, statsmodels) or R packages (tidyverse, vegan, KEGGREST, SYNCSA, UpSetR, ggpubr, pmartR) are missing or outdated; (4) reproducibility demands pin specific versions of MetaboDirect (e.g., v0.3.4 for benchmarking).

When NOT to use

• If MetaboDirect is already installed and verified with metabodirect -h — skip to data preparation and pipeline execution.
• If input is already a processed metabolomic feature table or molecular formula assignment (.csv format) — proceed directly to pipeline execution with metabodirect command, not installation.
• If targeting a system where system-level package management (conda, apt, Homebrew) conflicts with pip or manual R installation — consult the README and resolve environment conflicts first before attempting installation.

Inputs

• System with internet access for package downloads
• Python ≥3.5 installation
• R ≥4.0 installation
• Cytoscape ≥3.8 installation
• PyPI or GitHub repository access

Outputs

• Functional MetaboDirect command-line executable
• Installed Python dependencies (numpy, pandas, seaborn, py4cytoscape, statsmodels, more-itertools, argparse)
• Installed R packages (tidyverse, RColorBrewer, vegan, ggnewscale, ggpubr, KEGGREST, factoextra, UpSetR, pmartR, SYNCSA, ggvenn, ggrepel)
• Cytoscape with FileTransfer app enabled
• Environment configuration verified via metabodirect -h

How to apply

Install MetaboDirect via PyPI or from source by cloning the GitHub repository, ensuring Python ≥3.5, R ≥4.0, and Cytoscape ≥3.8 are present on the target system. Install all listed Python dependencies (argparse, numpy, pandas, seaborn, more-itertools, py4cytoscape, statsmodels) and R packages (tidyverse, RColorBrewer, vegan, ggnewscale, ggpubr, KEGGREST, factoextra, UpSetR, pmartR, SYNCSA, ggvenn, ggrepel). In Cytoscape, ensure the FileTransfer app is installed. Verify installation by running metabodirect -h to confirm the command-line interface is accessible. Document the installed version and environment details (OS, Python/R versions, package versions) for reproducibility and troubleshooting.

Related tools

• Python (Runtime environment and dependency manager for MetaboDirect core and package installation)
• R (Computational backend for statistical analysis, diversity metrics (vegan, SYNCSA), and visualization (ggpubr, ggnewscale))
• Cytoscape (Graph visualization and network analysis platform for biochemical transformation network generation and display)
• pip (Python package installer for MetaboDirect and Python dependencies)
• numpy (Numerical computation library for array operations in MetaboDirect data processing)
• pandas (Data manipulation and I/O library for handling Formularity .csv molecular formula tables)
• seaborn (Statistical data visualization library for generating plots and heatmaps in MetaboDirect)
• py4cytoscape (Python-to-Cytoscape bridge for programmatic network construction and visualization)
• vegan (R package for ecological diversity metrics (chemodiversity) calculation)
• KEGGREST (R package for querying KEGG database to obtain putative pathway and module annotations)
• SYNCSA (R package for calculating diversity metrics in MetaboDirect chemodiversity analysis)

Examples

pip install metabodirect && python -c 'import metabodirect; print("Installation successful")' && metabodirect -h

Evaluation signals

• Successfully execute metabodirect -h without errors; output displays command-line options and help text.
• Python import test: python -c 'import metabodirect; print(metabodirect.__version__)' returns version string (e.g., 0.3.4).
• Verify all Python dependencies are installed: pip show numpy pandas seaborn py4cytoscape statsmodels returns package information for each.
• Verify all R packages are installed: Rscript -e 'library(vegan); library(KEGGREST); library(SYNCSA)' completes without package loading errors.
• Test end-to-end: run metabodirect -h followed by metabodirect --version (if available) or a dry-run on sample data to confirm pipeline initialization.
• Check Cytoscape is accessible: Cytoscape should launch and FileTransfer app should be listed in app manager.

Limitations

• Installation requires internet access to download packages from PyPI and R CRAN repositories; offline environments need pre-cached packages.
• MetaboDirect requires both Python and R ecosystems, increasing system complexity and potential for version conflicts between language runtimes.
• R package pmartR (for normalization tests) may have compilation requirements on some systems; building from source can fail if system development tools are missing.
• Cytoscape 3.8+ and FileTransfer app installation are OS-specific and manual; no automated script provided in the README.
• Python 3.5 support (minimum specified version) is deprecated; testing on Python 3.8+ is recommended but not explicitly documented in the README.

Evidence

• [readme] MetaboDirect can be installed directly from PyPi using: pip install metabodirect: "MetaboDirect can be installed directly from PyPi using: pip install metabodirect"
• [readme] MetaboDirect requires Python (3.5 and above), R (4 and above) and Cytoscape (3.8 and above) with the following libraries/modules: "MetaboDirect requires Python (3.5 and above), R (4 and above) and Cytoscape (3.8 and above) with the following libraries/modules:"
• [methods] Install MetaboDirect (v0.3.4) via Python Package Index with dependencies NumPy, pandas, seaborn, py4cytoscape, and matplotlib, ensuring compatibility on the target OS (Windows, Linux, or MacOS).: "Install MetaboDirect (v0.3.4) via Python Package Index with dependencies NumPy, pandas, seaborn, py4cytoscape, and matplotlib, ensuring compatibility on the target OS (Windows, Linux, or MacOS)."
• [readme] Additionally it can be installed from source by cloning its GitHub repository: "Additionally it can be installed from source by cloning its GitHub repository"
• [readme] Information about the arguments can be obtaining using the option -h/--help: metabodirect -h: "Information about the arguments can be obtaining using the option -h/--help: metabodirect -h"
• [supplementary] The complete code for the MetaboDirect pipeline is freely available at its GitHub repository: https://github.com/Coayala/MetaboDirect: "The complete code for the MetaboDirect pipeline is freely available at its GitHub repository: https:// github.com/ Coaya la/ Metab oDire ct."