Singularity cheat sheet

// Create a Singularity image from a Docker image that is in the Docker hub
// where /tmp/ is the folder where the image will be created and ubuntu:14.04 
// is the docker image used to convert to the Singularity image
docker run \
-v /var/run/docker.sock:/var/run/docker.sock \
-v /tmp/:/output \
--privileged -t --rm \
singularityware/docker2singularity \
ubuntu:14.04
//
#Creating a singularity image from a docker image in docker hub:
singularity pull docker://elowy01/variant_filtering
# Then, we see that there will be a new file named file.simg containing the pulled image
# and we can run the pulled container by doing:
singularity run file.simg
//
#building a prebuilt docker image:
singularity build variant_filtering.simg docker://elowy01/variant_filtering
#where 'variant_filtering.simg' is the name that will be given to the image file
//
# Print all running container instances
singularity instance.list
//
#running a certain image
singularity run docker://elowy01/variant_filtering
//
# open an interactive shell using a certain image
 singularity shell variant_filtering.simg
 
//
# Knowing the singularity cachedir:
echo $SINGULARITY_CACHEDIR
# This cachedir will be used to store the docker images pulled from dockerhub