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
.