Installation

Docker

We provide a docker image to make the installation steps more convenient:

docker pull osvolo/anasfv:latest
docker container run -it osvolo/anasfv /bin/bash

Install requirements in conda environment and install ANASFV via PyPI

Requirements:

  1. python: 3.11 (tested). Most Python 3 versions should work.

  2. Software versions tested: - Samtools: 1.17 - BEDTools: 2.26.0 - Minimap2: 2.17 - Prodigal: 2.6.3 - Exonerate: 2.4.0 - BLAST: 2.12.0 - MUSCLE: 5.1 - Medaka: 1.11.3 - Homopolish: 0.4.1
    - uDance: 1.6.4

conda create -n anasfv -c conda-forge python=3.11 -y
conda activate anasfv
conda install -c bioconda samtools bedtools minimap2 prodigal exonerate blast muscle -y
pip install anasfv

If you need to use medaka and homopolish for polish, you need to create their corresponding conda environments and install them, because there will be some conflicts if you install them directly in the ANASFV runtime environment.

conda create -n medaka -c bioconda -c conda-forge medaka=1.11.3 -y
conda config --set channel_priority flexible
conda create -n homopolish -c conda-forge -c bioconda -c defaults more-itertools=8.4.0 homopolish=0.4.1 -y

The tree building process uses uDance. For uDance installation refer to uDance