salmon-docker-singularity

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

Salmon is a tool for quantifying the expression of transcripts using RNA-seq data
Dockerfile modified from https://github.com/COMBINE-lab/salmon/blob/master/docker/Dockerfile

Build docker container:

1. For salmon installation instructions:

https://combine-lab.github.io/salmon/getting_started/

2. Build the Docker Image

To build image from the command line:

# Assumes current working directory is the top-level salmon-docker-singularity directory
docker build -t salmon:1.9.0 .

Can do this on Google shell

To test this tool from the command line:

docker run --rm -it salmon:1.9.0 salmon -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 salmon-docker1.9.0.tar && gzip salmon-docker1.9.0.tar # = IMAGE_ID of salmon image
docker run -v "$PWD:/data" --rm -it singularity1.1.5 bash -c "singularity build /data/salmon1.9.0.sif docker-archive:///data/salmon-docker1.9.0.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 salmon.sif file to the system on which you want to run Salmon from the Singularity container

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

# set up path to the Salmon Singularity container
SALMON_SIF=path/to/salmon.sif

# Test that Salmon can run from Singularity container
singularity run $SALMON_SIF salmon -h # depending on system/version, singularity is now called apptainer

mattgalbraith/salmon-docker-singularity