Ubuntu — Códigos atualizados | Guia WSL ➜ Bioinfo

1) Atualizar sistema e instalar pacotes base

sudo apt update && sudo apt upgrade -y && sudo apt install -y build-essential git curl wget unzip parallel pigz python3-venv python3-tk

2) Instalar Miniforge (Conda) e ativar

wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
bash Miniforge3-Linux-x86_64.sh -b -p $HOME/miniforge3
$HOME/miniforge3/bin/conda init bash
exec bash

3) abritAMR + AMRFinderPlus (Conda) e DB

conda config --add channels conda-forge
conda config --add channels bioconda
conda create -n abritamr python=3.12 -y
conda activate abritamr
conda install -c bioconda -c conda-forge abritamr ncbi-amrfinderplus=3.12.8 blast parallel -y
amrfinder -u
export AMRFINDER_DB=$(ls -d $CONDA_PREFIX/share/amrfinderplus/data/* | sort | tail -n1)
echo 'export AMRFINDER_DB=$(ls -d $CONDA_PREFIX/share/amrfinderplus/data/* | sort | tail -n1)' >> ~/.bashrc

4) SPAdes / plasmidSPAdes

wget https://cab.spbu.ru/files/release3.15.5/SPAdes-3.15.5-Linux.tar.gz
tar -xzf SPAdes-3.15.5-Linux.tar.gz -C $HOME
export PATH=$HOME/SPAdes-3.15.5-Linux/bin:$PATH
echo 'export PATH=$HOME/SPAdes-3.15.5-Linux/bin:$PATH' >> ~/.bashrc
spades.py --version && plasmidspades.py --help

5) plasmid-screen (venv) + dependências

cd $HOME
git clone https://github.com/BCCDC-PHL/plasmid-screen.git
cd plasmid-screen
python3 -m venv .venv
source .venv/bin/activate
pip install -U pip
pip install -r requirements.txt
conda install -c bioconda -c conda-forge prokka blast -y
plasmid-screen --help

Dica: caminhos com espaços/acentos

mkdir -p $HOME/contigs_links
ln -s "/caminho/para/FASTA com espaços/"*.fasta $HOME/contigs_links/
cd $HOME/contigs_links
ls *.fasta | awk -v path="$PWD/" '{print $1 "\t" path $1}' > contigs.txt