ensemblorg/cpc2
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 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
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"
docker pull ensemblorg/cpc2