Share DSC via containers

First you need to install and configure docker:

  • Follow Docker installation guide until you can use sudo docker to print the “Hello World” example.
  • Run sudo usermod -aG docker $USER
  • Log out and log back in

We have provided a docker image for DSC which can be used to

  • Run some of the DSC vignettes examples
  • Serve as the base docker image to add to it your own benchmarks for others to reproduce.

Run DSC docker image demo

To use the docker image:

docker pull gaow/dsc
docker run --rm --security-opt label:disable \
       -v $USER:/home/docker -v /tmp:/tmp -v $PWD:$PWD \
       -t -P -w $PWD -u $UID:${GROUPS[0]} gaow/dsc \
       dsc -h

You can add a shortcut to your shell configuration script (~/.bashrc on Linux and ~/.bash_profile on Mac) to trigger docker based DSC:

alias dsc-docker='docker run --rm --security-opt label:disable -v $USER:/home/docker -v /tmp:/tmp -v $PWD:$PWD -t -P -w $PWD -u $UID:${GROUPS[0]} gaow/dsc dsc'

For example, to run the Introductory DSC tutorial,

cd ~/GIT/dsc/vignettes/one_sample_location

docker run --rm --security-opt label:disable -t -P -h DSC \
    -w $PWD -v $HOME:/home/$USER -v /tmp:/tmp -v $PWD:$PWD \
    -u $UID:${GROUPS[0]} -e HOME=/home/$USER -e USER=$USER gaow/dsc \
    dsc first_investigation.dsc --replicate 10 -c 2

INFO: Checking R library dscrutils@stephenslab/dsc/dscrutils ...
INFO: DSC script exported to first_investigation.html
INFO: Constructing DSC from first_investigation.dsc ...
INFO: Building execution graph & running DSC ...
DSC: 100%|######################################################################| 15/15 [00:19<00:00,  1.01s/it]
INFO: Building DSC database ...
INFO: DSC complete!
INFO: Elapsed time 21.425 seconds.

Use container options in DSC script to share your DSC

@CONF provides container and container_engine options to run DSC using containers (see this document for what @CONF does).

Set module specific container

The DSC scsript below uses docker image gaow/susie which has susieR package installed. If you have docker on your computer you should be able to run this module without having to install susieR.

susie: R(version = packageVersion('susieR'))
  $out: version
  @CONF: container = gaow/susie

dsc test.dsc --target susie

INFO: Load command line DSC sequence: susie
INFO: DSC script exported to test.html
HINT: Pulling docker image gaow/susie
INFO: Building DSC database ...
[###] 3 steps processed (3 jobs completed)
INFO: DSC complete!
INFO: Elapsed time 8.290 seconds.

Use singularity

To run the container with singularity instead of docker,

susie: R(version = packageVersion('susieR'))
  $out: version
  @CONF: container = gaow/susie, container_engine = singularity