fastxtoolkit-docker-singularity

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

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. http://hannonlab.cshl.edu/fastx_toolkit/index.html

Requirements:

Install within image using micromamba
https://github.com/mamba-org/micromamba-docker

Build docker container:

1. For FASTX Toolkit installation instructions:

http://hannonlab.cshl.edu/fastx_toolkit/download.html
https://bioconda.github.io/recipes/fastx_toolkit/README.html

2. Build the Docker Image

To build image from the command line:

# Assumes current working directory is the top-level fastxtoolkit-docker-singularity directory
docker build -t fastxtoolkit:0.0.14 . # tag should match software version

• Can do this on Google shell

To test this tool from the command line:

docker run --rm -it fastxtoolkit:0.0.14 fastx_uncollapser -h
docker run --rm -it fastxtoolkit:0.0.14 fastx_barcode_splitter.pl -h

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 fastxtoolkit0.0.14-docker.tar && gzip fastxtoolkit0.0.14-docker.tar # = IMAGE_ID of <tool> image
docker run -v "$PWD":/data --rm -it singularity:1.1.5 bash -c "singularity build /data/fastxtoolkit0.0.14.sif docker-archive:///data/fastxtoolkit0.0.14-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 fastxtoolkit0.0.14.sif file to the system on which you want to run FASTX Toolkit from the Singularity container

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

# set up path to the Singularity container
FASTXTOOLKIT_SIF=path/to/fastxtoolkit0.0.14.sif

# Test that FASTX Toolkit can run from Singularity container
singularity run $FASTXTOOLKIT_SIF fastx_uncollapser -h # depending on system/version, singularity may be called apptainer
singularity run $FASTXTOOLKIT_SIF fastx_barcode_splitter.pl -h