htseq2-docker-singularity

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

A Python library to facilitate programmatic analysis of data from high-throughput sequencing (HTS) experiments. A popular component of HTSeq is htseq-count, a script to quantify gene expression in bulk and single-cell RNA-Seq and similar experiments.

Build docker container:

1. For HTSeq installation instructions:

https://htseq.readthedocs.io/en/master/install.html
https://github.com/htseq/htseq/blob/master/README.md

2. Build the Docker Image

Docker image based on continuumio/miniconda3 and uses mamba + htseq_environment.yaml to install HTSeq 2 + dependencies

To build image from the command line:

# Assumes current working directory is the top-level htseq-docker-singularity directory
docker build -t htseq:2.0.2 .

• Can do this on Google shell

To test this tool from the command line:

docker run --rm -it htseq:2.0.2 htseq-count -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 htseq-docker2.0.2.tar && gzip htseq-docker2.0.2.tar # = IMAGE_ID of HTSeq image
docker run -v "$PWD:/data" --rm -it singularity:1.1.5 bash -c "singularity build /data/htseq2.0.2.sif docker-archive:///data/htseq-docker2.0.2.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 htseq.sif file to the system on which you want to run HTSeq from the Singularity container

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

# set up path to the HTSeq Singularity container
HTSEQ_SIF=path/to/htseq2.0.2.sif

# Test that HTSeq can run from Singularity container
singularity run $HTSEQ_SIF htseq-count -h # depending on system/version, singularity is now called apptainer