ensemblorg/cpc2 repository overview

⁠CPC2 Docker image

Dockerfile and commands to create the CPC2 Docker image and run it as a Singularity (tag 1.0.1).

Links: source code⁠, publication⁠

Docker image at Docker Hub: https://hub.docker.com/r/ftricomi/cpc2⁠

⁠Build and run the Docker image

Build the Docker image locally, using the Dockerfile

docker image build -t ftricomi/cpc2:latest .

or pull the existing image from DockerHub

docker pull ftricomi/cpc2

Run the image (see source code⁠ to set up the command for CPC2)

docker -v <working_dir> run ftricomi/cpc2:latest python3 /CPC2_standalone-1.0.1/bin/CPC2.py -i input.fa --ORF -o out.txt

⁠Run the Docker image as a Singularity

Pull the Docker image from DockerHub in the /hps/software/users/ensembl/genebuild/$USER/singularity directory, it will be saved as a Singularity image

singularity pull docker://ftricomi/cpc2:latest

Submit a job for running the Singularity image on LFS

bsub -M 4000 -R "rusage[mem=40000]" "singularity exec --bind <working_dir_absolute_path>:/app:rw /hps/software/users/ensembl/genebuild/$USER/singularity/cpc2.sif python3 /CPC2_standalone-1.0.1/bin/CPC2.py -i input.fa --ORF -o out.txt"