WSL — Códigos atualizados

Passo a passo no Windows 11 + WSL2, com comandos prontos e botões de copiar.

1) Instalar/atualizar o WSL (PowerShell como Administrador)

wsl --install -d Ubuntu-24.04
wsl --set-default-version 2
wsl --update
wsl --status
wsl -l -v

2) Configurar /etc/wsl.conf (systemd + montagens)

Dentro do Ubuntu (WSL):

printf "[boot]
systemd=true

[automount]
enabled=true
root=/mnt/
options="metadata,umask=22,fmask=11,uid=1000,gid=1000"
" | sudo tee /etc/wsl.conf

Reinicie o WSL (no Windows):

wsl --shutdown

3) Preparar o Ubuntu dentro do WSL

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

4) 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

5) abritAMR + AMRFinderPlus (Conda) e atualização do 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

6) Caminhos com espaços (OneDrive etc.): use symlinks

mkdir -p $HOME/contigs_links
ln -s /mnt/d/OneDrive/SEU/CAMINHO/COM\ ESPAÇOS/*.fasta $HOME/contigs_links/
cd $HOME/contigs_links
ls *.fasta | awk -v path="$PWD/" '{print $1 "\t" path $1}' > contigs.txt
abritamr run --contigs $PWD/contigs.txt --prefix ANALISE_AMR

7) 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

8) plasmid-screen (venv) + dependências

sudo apt install -y git python3-venv
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