bbtools-docker-singularity

Build Docker container for BBTools and (optionally) convert to Apptainer/Singularity.

BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.
The BBTools suite includes programs such as:
• bbduk – filters or trims reads for adapters and contaminants using k-mers
• bbmap – short-read aligner for DNA and RNA-seq data

Requirements:

To run BBTools, you need to have Java 7 or higher installed.

Build docker container:

1. For BBTools installation instructions:

https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/installation-guide/

2. Build the Docker Image

To build image from the command line:

# Assumes current working directory is the top-level bbtools-docker-singularity directory
docker build -t bbtools:39.01 . # tag should match software version

• Can do this on Google shell

To test this tool from the command line:

docker run --rm -it bbtools:39.01 java --version # verify java installation

docker run --rm -it bbtools:39.01 bbduk.sh --version # FAIL due to a bug in bbduk.sh when it should calculate memory usage (container only??) (also present in 38.90)
docker run --rm -it bbtools:39.01 bbduk.sh -Xmx500m --version # PASS specifying memory manualy (and may be better on HPC)
docker run --rm -it bbtools:39.01 bbduk.sh --help # PASS but help comes from the shell script and does not use java

docker run --rm -it bbtools:39.01 stats.sh --version # PASS
docker run --rm -it bbtools:38.90 bash -c "stats.sh in=/usr/local/bin/resources/phix174_ill.ref.fa.gz" # TEST with internal data - PASS so does not have same issue with memory calc

See issue here: https://www.biostars.org/p/372460/

Optional: Conversion of Docker image to Singularity

3. Build a Docker image to run Singularity

(skip if this image is already on your system)
https://github.com/mattgalbraith/singularity-docker

4. Save Docker image as tar and convert to sif (using singularity run from Docker container)

docker images
docker save <Image_ID> -o bbtools39.01-docker.tar && gzip bbtools39.01-docker.tar # = IMAGE_ID of BBTools image
docker run -v "$PWD":/data --rm -it singularity:1.1.5 bash -c "singularity build /data/bbtools39.01.sif docker-archive:///data/bbtools39.01-docker.tar.gz"

NB: On Apple M1/M2 machines ensure Singularity image is built with x86_64 architecture or sif may get built with arm64

Next, transfer the bbtools.sif file to the system on which you want to run BBTools from the Singularity container

5. Test singularity container on (HPC) system with Singularity/Apptainer available

# set up path to the BBTools Singularity container
BBTOOLS_SIF=path/to/bbtools39.01.sif

# Test that BBTools can run from Singularity container
singularity run $BBTOOLS_SIF bbduk.sh -Xmx500m --version # depending on system/version, singularity may be called apptainer