Installation - magwenelab/WeavePop GitHub Wiki
Requires a Linux operating system.
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
- Option 1: Download this GitHub repository
Use the green button <> Code and click Download ZIP.
Extract the .zip file to a directory called WeavePop/.
- Option 2: Use Snakedeploy (PENDING)
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/snakemake.yaml |
Snakemake,Python, Pandas |
workflow/envs/snakemake-apptainer.yaml |
Snakemake,Python, Pandas, Apptainer |
workflow/envs/snippy.yaml |
Snippy,Samtools |
workflow/envs/liftoff.yaml |
Litoff,Minimap2 |
workflow/envs/agat.yaml |
AGAT,Seqkit |
workflow/envs/samtools.yaml |
Samtools, Bedtools, Bcftools,Xonsh,Pandas, Click, SciPy, NumPy |
workflow/envs/depth.yaml |
Mosdepth |
workflow/envs/repeatmasker.yaml |
RepeatMasker,RepeatModeler, Bedtools, Seqkit |
workflow/envs/r.yaml |
R, tidyverse, svglite, scales, RColorBrewer |
workflow/envs/variants.yaml |
SnpEff,DuckDB, PyVCF, Xonsh,Pandas, Click, Biopython, Bedtools, Bcftools |
workflow/envs/pandas.yaml |
Pandas |
workflow/envs/shell.yaml |
Coreutils |