EMMA Docker Container

Instructions

Quickstart

docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere adamwilsonlab/emma:latest

Visit localhost:8787 in your browser and log in with username rstudio and the password you set. NB: Setting a password is now REQUIRED. Container will error otherwise.

Local machine (no password)

If you are running on a local machine with other security mechanisms, you can use the following:

docker run --rm \
  -p 127.0.0.1:8787:8787 \
  -e DISABLE_AUTH=true \
  adamwilsonlab/emma:latest

HPC

To use this container in an HPC environment like UB's CCR, you need to use singularity (a wrapper for docker that keeps things secure in a networked environment).

Singularity on UB's HPC

If you don't set these temp/cache folders you're likely to run out of space because the home directory doesn't have much room.

First log into a compute node. For example:

salloc --cluster=faculty --qos=adamw --partition=adamw  --job-name "InteractiveJob" --nodes=1 --ntasks=2 --mem=5G -C INTEL --time=05:20:00

# mount project folder inside container:
export PROJECT_FOLDER="/projects/academic/adamw/"

# define local working folder to build the SIF file (this is faster than network storage)
export APPTAINER_CACHEDIR="/scratch/"$USER"/singularity"

# path to singularity container file.  If you want to use a different image, you'll need
# to update this line.
export DOCKER_PATH="docker://adamwilsonlab/emma:latest"
export SIF_FILE="AdamWilsonLab-emma_docker-latest.sif"
export SIF_PATH=$PROJECT_FOLDER"/users/"$USER"/singularity/"

# Create the folders if they don't already exist
mkdir -p $PROJECT_FOLDER"/users/"$USER"/singularity"
mkdir -p $APPTAINER_CACHEDIR/tmp
mkdir -p $APPTAINER_CACHEDIR/run
mkdir -p $APPTAINER_CACHEDIR/rstudio

# go to cachedir for faster build
cd $APPTAINER_CACHEDIR


## Build the singularity image (.SIF) directly from Docker image locally
### If it takes too long, you can use `nohup` first to allow it to keep running if the SSH connection is broken.

singularity build --force $SIF_FILE $DOCKER_PATH &

# Move it to it's permanent home
mv $SIF_FILE $SIF_PATH

Accessing the image for interactive computation

1. SSH to vortex.ccr.buffalo.edu and then request an interactive job with something like:

salloc --cluster=faculty --qos=adamw --partition=adamw  --job-name "InteractiveJob" --nodes=1 --ntasks=2 --mem=5G -C INTEL --time=05:20:00

Then run the following to start using R from the container:

export PROJECT_FOLDER="/projects/academic/adamw/"
export APPTAINER_CACHEDIR="/scratch/"$USER"/singularity"
export SIF_PATH=$PROJECT_FOLDER"/users/"$USER"/singularity"
export SIF_FILE="AdamWilsonLab-emma_docker-latest.sif"


singularity run \
      --bind $PROJECT_FOLDER:$PROJECT_FOLDER \
      --bind $APPTAINER_CACHEDIR/tmp:/tmp \
      --bind $APPTAINER_CACHEDIR/run:/run \
      $SIF_PATH/$SIF_FILE R

2. Use CCR's OnDemand portal