Building asap_run

Edit new Dockerfile.vX Update Dockerfile symlink Edit image tag in docker-compose.yml

docker-compose build

OLD

asap_run

ASAP container for running all pipeline code

How to build the latest asap_run Docker from this git clone

docker build . -t asap_run:v8

How to use pre-built Docker images

All pre-built images for asap-run are available on DockerHub. You can pull any version by using the pull commmand:

docker pull fabdavid/asap_run:v7

How to run a command from a container:

• You can open a shell in a Docker, and for example run "Rscript" from within the container

docker run -it fabdavid/asap_run:v8 bash

Then run

Rscript myscript.R

• You can also directly run the command from within the container, but without entering the container per se

docker run --rm fabdavid/asap_run:v8 Rscript myscript.R

Note: Use the -v option to mount any volume on the Docker container, so that you can access the necessary files

How to extract the list of R package versions from a docker

grep -Ri "^version:" /usr/local/lib/R/library/ | grep DESCRIPTION