Prolipipe : large-scale assessment of metabolic profiles on bacteria focusing on specific pathways.

Assessing capacity to synthesize or degrade specific compounds among a large set of bacterial metabolic networks and screen them accordingly.

Table of contents

• License
• Installation
  • Dependencies
  • conda
• Usage

License

This workflow is licensed under the GNU GPL-3.0-or-later, see the LICENSE file for details.

Installation

Dependencies

Prolipipe relies on outputs from the "AuFAMe" package It runs with python >= 3.8.

These python packages are needed :

• pandas
• numpy
• plotly
• glob2
• jupyter
• papermill
• padmet

Prolipipe also needs Quarto to generate the interactive report (version > 1.7).

conda

Prolipipe is available on the conda channel "fermentsdufutur" and can be installed with:

conda create -n prolipipe
conda activate prolipipe
conda install -c fermentsdufutur prolipipe

Usage

To run Prolipipe with padmet files from AuFAMe as input, generate TSV files and an interactive Quarto report:

prolipipe -pad DIRECTORY --tax TAXFILE --pwy PWY_FOLD

To generate TSV files without the Quarto report:

prolipipe -pad DIRECTORY --tax TAXFILE --pwy PWY_FOLD --no-report

To run Prolipipe with TSV files from AuFAMe as input and generate an interactive Quarto report:

prolipipe -i DIRECTORY --tax TAXFILE --pwy PWY_FOLD

To regenerate Quarto report from TSV files created by Prolipipe:

prolipipe-report -i DIRECTORY -d OUT_DIRECTORY