A barebones docker container to run remotePARTS.

Copy the docker image from this repo or pull the docker container from the docker hub

docker pull kelewinska/rparts:latest

Build the docker image:

# the '-t' flag passes the name of the container in the local environment
docker build -t kelewinska/rparts:<version-tag>

Run docker image kelewinska/rparts:<version-tag> in an interactive container named rparts :

docker run -it --name rparts kelewinska/rparts:<version-tag>

Run docker image kelewinska/rparts:<version-tag> in an interactive container named rparts with additional volumes mounted:

docker run -v /data:/data -v /mnt:/mnt -w $PWD -u $(id -u):$(id -g) -it --name rparts kelewinska/rparts:<version-tag>

Use appropriate --user, --volume, --workdir options to define user-specific settings, to mount volumes necessary for the processing, and to define working directory inside the container, respectively. Be careful with using $PWD - when used, it makes a container nonindependent from the local environment. The use of --cpus can be desired to limit CPUs use allowed for a container. Or even better --cpuset-cpus to indicate the cpus available for a container (their use will be maxed out according to the processing done in a container).

docker run -v /data:/data -v /mnt:/mnt -u $(id -u):$(id -g) -it `--cpuset-cpus`="0-19" --name rparts kelewinska/rparts:<version-tag>

For better experience, please add to the docker image R packages essential for your specific workflow(s).

The current :latest image is build based on r-base:4.3.1.