pantools-pipeline-v4

General purpose Snakemake pipeline for PanTools v4.

This pipeline can be used to run PanTools code for specific use cases and datasets.

Requirements: Snakemake, Mamba.

Cloning this git

For cloning this git, run:

git clone https://github.com/PanUtils/pantools-pipeline-v4
cd pantools-pipeline-v4

Install Snakemake and Mamba

If you don't have mamba, install it using

conda install -n base -c conda-forge mamba

Then, a Snakemake environment can be created using

conda activate base
mamba create -c conda-forge -c bioconda -n snakemake snakemake

Which can be activated and verified with

conda activate snakemake
snakemake --help

Running the pipeline

Run the pipeline

The pipeline can be run with

snakemake [rule] --use-conda --cores <threads> [--configfile <config>] [--conda-prefix <prefix>] [--until <function>]

threads: number of threads to use.
config: custom configuration file.
prefix: path to directory containing conda environments for reuse.
function: name of a pantools function, the pipeline stops if this function is complete. \

If no config is provided, the pipeline will run on a small yeast test dataset. The possible rules are discussed below. The pipeline will run all major PanTools functions for a pangenome if no rules are specified.

Rules

all_pangenome

Create a pangenome and run all major PanTools analysis functions for pangenomes.

all_panproteome

Create a panproteome and run all major PanTools analysis functions for panproteomes.

panva

Create a pangenome and run all PanTools analysis functions required to make a PanVa instance.