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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

Singularity

There are two methods to pull the docker image into Singularity as explained below.

Set some useful environment variables

If you don't do this you're likely to run out of space because the home directory doesn't have much room.

# mount project folder inside container:
export PROJECT_FOLDER="/projects/academic/adamw/"
# 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 CONTAINER_PATH="/vscratch/grp-adamw/singularity/$USER/AdamWilsonLab-emma_docker:latest.sif"
# to use for ssh:
export SERVER_URL="horae.ccr.buffalo.edu"
# folder to hold temporary singularity files - unique for each user:
# export SINGULARITY_LOCALCACHEDIR="/panasas/scratch/grp-adamw/singularity/"$USER
export SINGULARITY_LOCALCACHEDIR="/ssd_data/singularity/"$USER

# name the resulting sif file
export SIF_PATH=$SINGULARITY_LOCALCACHEDIR/"AdamWilsonLab-emma_docker-latest.sif"

# define a few more folders used by singularity
export SINGULARITY_CACHEDIR=$SINGULARITY_LOCALCACHEDIR
export SINGULARITY_TMPDIR=$SINGULARITY_LOCALCACHEDIR

# Create the folders if they don't already exist
mkdir -p $SINGULARITY_LOCALCACHEDIR/tmp
mkdir -p $SINGULARITY_LOCALCACHEDIR/run
mkdir -p $SINGULARITY_LOCALCACHEDIR/rstudio

Build directly from Docker image locally

Build the .sif directly from the docker image.

# build the singularity image - note this takes about 3 hours on horae!
nohup singularity build --force $SIF_PATH $DOCKER_PATH &

The nohup simply allows it to keep running if the SSH connection is broken.

Then follow the singularity_start.sh script.

Use the precompiled .sif from Github

A .sif file is compiled using github actions when the version number of the image is updated in this repository. These can be found here. However, they are only produced if turned on in the GitHub actions builder.yml file.

You will only need to run the following once (unless the image changes).

mkdir -p /vscratch/grp-adamw/singularity/adamw
cd /vscratch/grp-adamw/singularity/adamw
rm AdamWilsonLab-emma_docker-latest.sif
wget -O $SIF_PATH https://github.com/AdamWilsonLab/emma_docker/releases/download/0.0.530/AdamWilsonLab-emma_docker-latest.sif.zip
unzip $SIF_PATH

Then follow the singularity_start.sh script.