subread-docker-singularity

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

The Subread package comprises a suite of software programs for processing next-gen sequencing read data including Subread, featureCounts, Sublong.
https://subread.sourceforge.net/
http://bioconductor.org/packages/release/bioc/html/Rsubread.html

Requirements:

See Dockerfile for build requirements
To run: Python2 interpreter in PATH

Build docker container:

1. For Subread installation instructions:

https://github.com/ShiLab-Bioinformatics/subread#readme

2. Build the Docker Image

To build image from the command line:

# Assumes current working directory is the top-level subread-docker-singularity directory
docker build -t subread:2.0.4 . # tag should match software version

• Can do this on Google shell

• Alternative build using Bioconda/µmamba (Currently up to 2.0.3 available):

# Assumes current working directory is the top-level subread-docker-singularity directory
docker build -t subread:2.0.3 -f Dockerfile_micromamba . # tag should match software version

To test this tool from the command line:

docker run --rm -it subread:2.0.4 featureCounts -v

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 subread2.0.4-docker.tar && gzip subread2.0.4-docker.tar # = IMAGE_ID of Subread image
docker run -v "$PWD":/data --rm -it singularity:1.1.5 bash -c "singularity build /data/subread2.0.4.sif docker-archive:///data/subread2.0.4-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 subread2.0.4.sif file to the system on which you want to run Subread from the Singularity container

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

# set up path to the Singularity container
SUBREAD_SIF=path/to/subread2.0.4.sif

# Test that Subread can run from Singularity container
singularity run $SUBREAD_SIF featureCounts -v # depending on system/version, singularity may be called apptainer