kbessonov/mob_suite repository overview

A fully functional image containing the latest MOB-Suite for plasmid typing. For more information refer to https://github.com/phac-nml/mob-suite⁠.

To run analysis:

a) pull desired image

docker pull kbessonov/mob_suite:<tag> where tag is a mob_suite version e.g. docker pull kbessonov/mob_suite:3.0.3

b) run the mob-suite inside docker container in mounted directory

docker run -v <path2dir>:/mob-suite --rm kbessonov/mob_suite:3.0.3 bash -c "cd mob-suite && mob_typer -i plasmid.fasta -o plasmid-report.txt" where path2dir is a path on your LOCAL directory containing sequences and /mob-suite is a mounted directory inside the docker container. To run other mob_suite tools, modify the bash command.

To convert this image to Singularity format

• docker pull kbessonov/mob_suite:<tag> or
• docker run -v /var/run/docker.sock:/var/run/docker.sock -v /tmp/mob_suite_image:/output --privileged -t --rm singularityware/docker2singularity kbessonov/mob_suite:3.0.3 (the resulting squashfs read-only sif image will be saved in /tmp/mob_suite_image directory on your host).
• For writable ext3 image docker run -v /var/run/docker.sock:/var/run/docker.sock -v /tmp/mob_suite_image:/output --privileged -t --rm singularityware/docker2singularity --writable kbessonov/mob_suite:3.0.3
• To convert read-only sif singularity image to writable sandbox directory run docker run -it --rm singularityware/singularity build --sandbox mob_suite_3.0.3/ mob_suite_3.0.3.sif (this will create mob_suite_3.0.3 directory that can be run in singularity by singularity shell --writable mob_suite_3.0.3/)

Lite image versions (marked as lite suffix) do not contain initialized databases to save on image space. Mount necessary databases using -d parameter.