pmambrose / docker-bowtie2

Bowtie2 v2.5.2 Dockerfile Native for Apple M1+ Silicon (ARM64) and Intel/AMD (x86_64) Containers

Bowtie2 v2.5.2 Dockerfile Native for Apple M1+ Silicon (ARM64) and Intel/AMD (x86_64) Containers

This repository contains a Dockerfile for Bowtie2 version 2.5.2 (released on October 14, 2023) specifically designed to detect the computer architecture and create a native Docker container image for either Apple M1/2/3+ Silicon (ARM64) or Intel/AMD (x86_64) chips.

Overview

Bowtie2 is a popular tool for aligning sequencing reads to long reference sequences. This Dockerfile automates the installation of Bowtie2 in a Docker container, ensuring a consistent and reproducible environment for genomic analysis.

Features

• Architecture Detection: Automatically detects the host's CPU architecture (ARM64 or x86_64) and builds a native compatible Docker image. For example, a docker image built on Apple M1/2/3+ Silicon computers will contain bowtie2 and all dependencies natively compiled for Apple's arm64 architecture, which precludes the need for a Rosetta2 emulation layer, boosting performance and also minimizing the risk of emulator compatibility errors and ensuring uninterrupted compatibility if Apple drops Rosetta2 support in future OSX updates.
• Optimized for Bowtie2 v2.5.2, Released Oct 14, 2023: Specifically tailored for version 2.5.2 of Bowtie2 and includes all version-specific dependencies (eg. bowtie2 v2.5.2 requires python3 version >=3.10 & <3.11.0a0)
• Easy to Use: Simplifies the process of setting up Bowtie2, especially on systems with compatibility issues.

Prerequisites

• Docker installed on your machine. Easiest way to do this is by installing Docker Desktop.
• Basic knowledge of Docker commands. Examples are given below.

Usage

1. Clone the Repository:

   git clone https://github.com/pmambrose/docker-bowtie2.git
   cd docker-bowtie2

• Alternatively you can also download the repository as a zip file, unpack, and then enter the directory in terminal.

2. Build the Docker Image:

• The Dockerfile will automatically detect the CPU architecture and build the appropriate native container image.

  bash ./build_docker_bowtie2.sh

3. Run Bowtie2 in the Container::

• In the general case, you can run bowtie2 commands in your terminal using the following template. Replace command with your desired Bowtie2 command (as you would in a native terminal, starting with bowtie2 for example) and /your/data/path with your data directory. Since the bowtie2 container will reference the internal directory (/home which points to /your/data/path), adjust commands to point to files relatve to the container's /home directory. See examples below for more details.

  docker run -v /your/data/path:/home bowtie2-docker /bin/bash -c "command"

• We can run a simple test in which we create and enter a docker container created from our bowtie2-docker image and then run bowtie2-help in terminal:

  docker run -it --name my_bowtie2_container bowtie2-docker  
  bowtie2 --help

• Which produces the following output in terminal:

  pradeep@Pradeeps-MacBook-Pro ~ % docker run -it --name my_bowtie2_container bowtie2-docker  
  root@40458769aa0b:/# bowtie2 --help
  Bowtie 2 version 2.5.2 by Ben Langmead ([email protected], www.cs.jhu.edu/~langmea)
  Usage: 
  bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | -b <bam>} [-S <sam>]

Examples

Here are some real-world examples of how I use this docker container within my workflow. Here, my terminal working directory ./ is set to the container's /home directory and the commands are run from within a bash script.

1. Generate a Bowtie2 Index For Alignments:

• To generate a small index using a poliovirus.fasta file in the terminal's working directory into a relative path directory ./alignments/index/, while piping bowtie2's terminal output during index building to indexing_terminal.txt:

  docker run -v ./:/home bowtie2-docker /bin/bash -c "bowtie2-build /home/poliovirus.fasta /home/alignments/index/poliovirus > /home/alignments/index/indexing_terminal.txt"

2. Align using Bowtie2:

• To align a compressed fastq file (with local relative path ./data/1_consensus.fastq.gz) using the above sequence index and output as a compressed sam file (with local relative path ./alignments/2_alignment.sam.gz), running Bowtie2 multi-threaded using 4 CPU threads:

   docker run -v ./:/home bowtie2-docker /bin/bash -c "bowtie2 -q --phred33 --threads 4 --no-hd --no-sq --local -x /home/alignments/index/poliovirus -U /home/data/1_consensus.fastq.gz | gzip -c > /home/alignments/2_alignment.sam.gz"

Customization

• Environment Variables: Modify any necessary environment variables in the Dockerfile.

• Additional Dependencies: Add any additional dependencies required for your specific workflow.

Contributing

Contributions to improve the Dockerfile or address issues are welcome. Please submit a pull request or open an issue to discuss potential changes.

License

This Dockerfile is distributed under the MIT license.

Contact

For help or feedback, please contact me at [email protected].

Acknowledgements

• Thanks to Benjamin Langmead and the Bowtie2 team for developing and maintaining the software.