Conda environment setup guide

This guide will help you install Miniconda and set up the bioinformatics environment for the training.

What is Conda?

Conda is a package and environment management system that makes it easy to install bioinformatics software and manage dependencies.

Installing Miniconda

For Linux/WSL

# Download Miniconda installer
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

# Run the installer
bash Miniconda3-latest-Linux-x86_64.sh

# Follow the prompts:
# - Press Enter to review license
# - Type 'yes' to accept
# - Press Enter to confirm installation location
# - Type 'yes' to initialise Miniconda

# Activate conda
source ~/.bashrc

# Verify installation
conda --version

For macOS

# Download Miniconda installer
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh

# Run the installer
bash Miniconda3-latest-MacOSX-x86_64.sh

# Follow the same prompts as Linux
source ~/.bashrc
conda --version

Configuring Conda

Add Bioconda and Conda-Forge channels

# Add channels in the correct order
conda config --add channels conda-forge
conda config --add channels bioconda

# Verify channels
conda config --show channels

Creating the training environment

Method 1: Manual Installation

# Create a new environment with Python
conda create -n pathogen_detection python=3.9 -y

# Activate the environment
conda activate pathogen_detection

# Install bioinformatics tools
conda install -c bioconda fastqc multiqc nanoplot porechop fastp minimap2 samtools kraken2 krona flye medaka quast abritamr  -y

# Install additional tools
conda install -c conda-forge wget curl csvtk parallel -y

# Install amrfinderplus separately
conda install -y -c conda-forge -c bioconda --strict-channel-priority ncbi-amrfinderplus

Method 2: Using environment.yml file

Use the pathogen_detection.yml file provided in the repository to create the environment with all required packages.

# create pathogen_detection.yml
nano pathogen_detection.yml

# Create environment from file
conda env create -f pathogen_detection

# Activate the environment
conda activate pathogen_detection

Troubleshooting

Issue: Conda command not found

Solution:

# Re-initialize conda
source ~/miniconda3/bin/activate
conda init bash
source ~/.bashrc

Issue: Slow package installation

Solution:

# Use mamba (faster alternative to conda)
conda install mamba -c conda-forge -y
mamba install <package-name>

Issue: Package conflicts

Solution:

# Create clean environment
conda create -n pathogen_detection_clean python=3.9 -y
conda activate pathogen_detection_clean
# Install packages one by one

Issue: Permission errors

Solution:

# Don't use sudo with conda
# If you installed Miniconda with sudo, reinstall without it

Additional Resources

• Conda Documentation
• Bioconda
• Conda-forge documentation
• Mamba Documentation