snp_tree.sh

#/usr/bin/env bash
set -e
ENV=snp_tree
source miniconda3/etc/profile.d/conda.sh
if !(conda info --envs | grep $ENV); then
    echo "Installing dependencies..."
    # conda config --add channels defaults
    # conda config --add channels bioconda
    # conda config --add channels conda-forge
    conda create --name $ENV python=3.9 mafft snp-sites snp-dists quicktree -q -y
    conda activate $ENV
    pip install bio pandas
    wget https://gist.githubusercontent.com/fredyr/5bff0d4a3fdc7fc41512791351b2da51/raw/f26ed9e5c52b161bb5df49462d2e1e67f7f470b1/snp-dists_phylip.py
    conda deactivate
    echo "Installation done!"
    echo "Run with: "
    echo "./snp_tree.sh <prefix> *.consensus.fa"
    exit 0
else
    echo
    echo "Dependencies installed, running pipeline..."
fi

conda activate $ENV
prefix=$1; shift 1
FA=$@
if [ ! -f "$prefix.nwk" ]; then
    cat $FA > $prefix.cns.fa
    mafft $prefix.cns.fa > $prefix.aln.fa
    snp-sites -c $prefix.aln.fa > $prefix.core.fa
    snp-dists $prefix.core.fa | python snp-dists_phylip.py > $prefix.phylip
    quicktree -in m $prefix.phylip > $prefix.nwk
    echo "Newick tree written to $prefix.nwk"
fi