Red Docker image

Dockerfile for generating a Docker image for Red, "an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale".

Links: source code⁠, publication⁠

Docker image at Docker Hub: https://hub.docker.com/r/williamebi/red

notes

The Dockerfile in the root of this directory compiles a Red binary from source code, whereas the Dockerfile in the use_existing_binary directory downloads the pre-compiled binary provided by the developer of Red. Normally the pre-compiled binary would be used, but since these two Dockerfiles have been created as examples, the one with compiling a binary from scratch is included as well. For future production images only a single Dockerfile is needed.

build, publish, and run a Docker image

build a Docker image

docker image build -t williamebi/red:2.0 .

run the Docker image locally

# print the help message
docker run williamebi/red:2.0

# run repeat masking
docker run williamebi/red:2.0 -gnm <genome_directory> -msk <output_directory>

upload the Docker image to Docker Hub (you need an account and to log in with docker login)

docker push williamebi/red:2.0

run the Docker image directly with Singularity on a compute or login node

singularity run docker://williamebi/red:2.0 -gnm <genome_directory> -msk <output_directory>"

generate a Singularity image from the Docker image at Docker Hub, which will be saved in the /hps/nobackup2/singularity/$USER directory

singularity pull docker://williamebi/red:2.0

run the Singularity image on a compute or login node

singularity run "/hps/nobackup2/singularity/$USER/red-2.0.simg"

submit a job for running the Singularity image on LFS

bsub -I -M10000 -R"select[mem>10000] rusage[mem=10000]" "singularity run /hps/nobackup2/singularity/$USER/red-2.0.simg -gnm <genome_directory> -msk <output_directory>"