bneron/crispr repository overview

⁠CRISPRCasFinder

⁠how to use CRISPRCasFinder container with docker

The computation are perform under crispr user in /home/crispr inside the container. So You have to mount a directory from the host in the container to exchange data (inputs data, and results) from the host and the container.

not that the -in path is the path inside the container In the host the path to data is /home/login/Projects/GEM/CRISPRCasFinder-release-4.2.20/install_test/sequence.fasta The /home/login is mounted in /home/crispr in the container So the path of data in the container is /home/crispr/Projects/GEM/CRISPRCasFinder-release-4.2.20/install_test/sequence.fasta

 docker run -v $HOME:/home/crispr -u $(id -u ${USER}):$(id -g ${USER}) bneron/crispr -in /home/crispr/Projects/GEM/CRISPRCasFinder-release-4.2.20/install_test/sequence.fasta  -cas -log  -ccc 20000 -ccvRep -keep  -rcfowce -def S -cpuM 4  -cf CasFinder-2.0.3

⁠how to use with singularity

As the docker image is registered in docker hub you can also use it directly with Singularity⁠. Unlike docker you have not to worry about shared directory, your home and /tmp are automatically shared.

singularity pull --name crispr.simg docker://bneron/crispr

singularity run crispr.simg -in ~/Projects/GEM/CRISPRCasFinder-release-4.2.20/install_test/sequence.fasta  -cas -log  -ccc 20000 -ccvRep -keep  -rcfowce -def S -cpuM 4  -cf CasFinder-2.0.3