Environment

Tutorial: Using Mamba and Bioconda for Bioinformatic Research

This guide provides step-by-step instructions for setting up and using Mamba and Bioconda to manage bioinformatics software and environments.

Prerequisites

  • Basic command-line knowledge (Linux/macOS/Windows WSL).
  • Miniconda or Anaconda installed. Download Miniconda.

Step 1: Install Mamba

Mamba is a faster alternative to Conda. Install it with:

  • conda install mamba -n base -c conda-forge

Verify the installation:

  • mamba --version

Step 2: Set Up Bioconda

Bioconda provides bioinformatics tools. Configure it:

  1. Add channels:
    • conda config --add channels defaults
    • conda config --add channels bioconda
    • conda config --add channels conda-forge
  2. Set strict channel priority:
    • conda config --set channel_priority strict
  • Verify:
    • conda config --show channels

Step 3: Create a Bioinformatics Environment

Create and activate an environment with tools like fastqc:

  • mamba create -n bioenv fastqc
  • conda activate bioenv
  • fastqc --version

Step 4: Install Additional Tools

Install more tools (e.g., bwa, samtools, bcftools):

  • mamba install bwa samtools bcftools

Verify installations:

  • bwa
  • samtools --version
  • bcftools --version

Step 5: Search for Bioconda Packages

Search and install tools (e.g., bowtie2):

  • mamba search bowtie2
  • mamba install bowtie2

Step 6: Update and Manage Environments

  1. Update all packages:
    • mamba update --all
  2. Remove a package:
    • mamba remove fastqc
  3. Deactivate the environment:
  4. conda deactivate
  5. Remove an environment:
    • conda env remove -n bioenv

Step 7: Export and Share Environments

Export an environment to a YAML file:

  • conda activate bioenv
  • conda env export > bioenv.yml

Recreate the environment:

  • conda env create -f bioenv.yml

Step 8: Use Mamba in Scripts

Example script for a workflow:

  • #!/bin/bash
  • # Create environment
    mamba create -n workflow_env -y fastqc bwa samtools
  • # Activate environment
    conda activate workflow_env
  • # Run analysis
    fastqc input.fastq
    bwa index reference.fasta
    bwa mem reference.fasta input.fastq > output.sam
    samtools view -b output.sam > output.bam
  • # Deactivate environment
    conda deactivate

Best Practices

  1. Use Mamba for faster installations.
  2. Keep environments modular for different projects.
  3. Regularly update packages with mamba update --all.
  4. Share environments using YAML files.