Installation

Requires a Linux operating system.

1) Install Conda

Install Mamba or Miniconda following the instructions from their webpage:

• Mamba: https://github.com/conda-forge/miniforge (recommended)
• Miniconda: https://docs.anaconda.com/miniconda/

After successfully installing conda, add the necessary channels and set strict channel priority by running:

conda config --add defaults
conda config --add conda-forge
conda config --add bioconda
conda config --set channel_priority strict

2) Download the workflow

• Option 1: Download this GitHub repository

Go to Releases and download the source code of the latest one.

• Option 2: Use Snakedeploy

Follow the instructions in the Snakemake Workflow Catalog

3) Install the Snakemake Conda environment

In a terminal go to the directory WeavePop/ and run:

mamba env create --file workflow/envs/snakemake.yaml # use conda instead of mamba if you installed Miniconda

The environments for particular software used by the pipeline will be installed by Snakemake when you run it, so you don't need to install them. The programs in each environment are described in the table below.

Software in the environments used in the pipeline

Environment files	Software
workflow/envs/agat.yaml	AGAT,Seqkit
workflow/envs/depth.yaml	Mosdepth
workflow/envs/liftoff.yaml	Litoff,Minimap2
workflow/envs/pandas.yaml	Pandas
workflow/envs/r.yaml	R, tidyverse, svglite, scales, RColorBrewer, scales, ggnewscale, patchwork, ggbeeswarm, ggrepel
workflow/envs/repeatmasker.yaml	RepeatMasker,RepeatModeler
workflow/envs/samtools.yaml	Samtools, Bedtools, Bcftools,Xonsh,Pandas, SciPy, NumPy
workflow/envs/shell.yaml	Coreutils
workflow/envs/snakemake-apptainer.yaml	Snakemake,Python, Pandas, Apptainer
workflow/envs/snakemake.yaml	Snakemake,Python, Pandas
workflow/envs/snippy.yaml	Snippy,Samtools
workflow/envs/variants.yaml	SnpEff,DuckDB, PyVCF, Xonsh,Pandas, Biopython, Bedtools, Bcftools