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:https://bioconductor.org/packages/release/bioc/html/Rsubread.html
See Dockerfile for build requirements
To run: Python2 interpreter in PATH
https://github.com/ShiLab-Bioinformatics/subread#readme
# Assumes current working directory is the top-level subread-docker-singularity directory
docker build -t subread:2.0.4 . # tag should match software version
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Can do this on Google shell
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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
docker run --rm -it subread:2.0.4 featureCounts -v
(skip if this image is already on your system)
https://github.com/mattgalbraith/singularity-docker
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:https:///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
# 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