The Prolipipe pipeline is about genome annotation and metabolic pathway reconstruction. From .fasta genomes, it enables to find if strains of bacteria are theorically able to produce metabolites.

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

Because of the amount of calculations, we advise to create a genouest account and install all the requirements on your cluster account.
We advise you to create a conda environment with bioperl 5.22 (not above) to be able to use prokka.
You may have to install python and the followng packages : optparse, matplotlib.pyplot, pandas, numpy, csv.

You can install prokka many ways, as described in the prokka github page. We used version 1.12.

To install and use pathway tools and mpwt with singularity, you can follow the tutorial of Metage2Metabo here

We used version 2.1.9 of eggnog-mapper and the associate database, version 5.0.2. You can install eggnog-mapper with pip : pip install eggnog-mapper

To begin, you can download genomes using ncbi genome download or use your own ones.
The genomes must be ordonned like the genome folder in toy_example.

pipeline.py --argument [argument]

mandatory arguments :

--input		Path to the folder where the genomes are
--padmet_ref	Path to the reference database in Padmet format
--output	Path to the folder where you want to put the results in
--ptsc		Path to the root folder
--ptsi		Name of the singularity image
--tax		Path of the all_taxon.tsv file
--pwy		Path to the folder with the pathways.txt files for all wanted metabolites

options :

-a		Launch the creation of the askomics files
--strain	Path to the strain file (name of strain and status), mandatory with option -a
--annot		Annotation tool : 'prokka' or 'eggnog'. (Default is prokka)
--egg_path	Path to the eggnop database, mandatory if you choose eggnog as the annotation tool
-r		Renames all the strains with abreviations
-k		Keep .faa files that can be need to use other annotation software like eggNOG-mapper
-v		Activate verbose  

Before launching the pipeline, please make sure you have completed the all_taxons.tsv file with the information of your own genomes and that you have created (at least) one .txt file which contains a list of metacyc reaction corresponding to a pathway, as in the pathway_pyruvate.txt file.