rseqc-docker-singularity

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

The RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.
https://rseqc.sourceforge.net/

Requirements:

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

Build docker container:

1. For RSeQC installation instructions:

https://rseqc.sourceforge.net/#installation
https://bioconda.github.io/recipes/rseqc/README.html

2. Build the Docker Image

To build image from the command line:

# Assumes current working directory is the top-level rseqc-docker-singularity directory
docker build -t rseqc:5.0.1 . # tag should match software version

• Can do this on Google shell

To test this tool from the command line:

docker run --rm -it rseqc:5.0.1 bam_stat.py --help # or any other RseQC script

BED format gene annotations used by RseQC

Housekeeping genes

(required by geneBody_coverage.py, tin.py)
Human: https://sourceforge.net/projects/rseqc/files/BED/Human_Homo_sapiens/hg38.HouseKeepingGenes.bed.gz
Mouse: https://sourceforge.net/projects/rseqc/files/BED/Mouse_Mus_musculus/mm10.HouseKeepingGenes.bed.gz

All genes

(required by infer_experiment.py, inner_distance.py, junction_annotation.py, junction_saturation.py, read_distribution.py)
Human: https://sourceforge.net/projects/rseqc/files/BED/Human_Homo_sapiens/
or from UCSC Table Browser
Mouse: https://sourceforge.net/projects/rseqc/files/BED/Mouse_Mus_musculus/
or from UCSC Table Browser

To get the most recent annotation and gene models for other species, use UCSC's Table Browser https://genome.ucsc.edu/cgi-bin/hgTables?command=start
Make sure the gene model and the genome assembly are matched.

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 rseqc5.0.1-docker.tar && gzip rseqc5.0.1-docker.tar # = IMAGE_ID of rseqc image
docker run -v "$PWD":/data --rm -it singularity:1.1.5 bash -c "singularity build /data/rseqc5.0.1.sif docker-archive:///data/rseqc5.0.1-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 rseqc5.0.1.sif file to the system on which you want to run RseQC from the Singularity container

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

# set up path to the Singularity container
RSEQC_SIF=path/to/rseqc5.0.1.sif

# Test that RseQC scripts can run from Singularity container
singularity run $RSEQC_SIF bam_stat.py --help # depending on system/version, singularity may be called apptainer