launch.sh

#!/bin/bash

LOCAL_ENV=.local_env
CREATE_ENV=false

usage() {
	cat <<EOF
USAGE: launch.sh

launch utility script
----------------------------------------

launch.sh [command]
	build
	bash
	setup
	container
	jupyter
EOF
	exit
}


if [ -e ./$LOCAL_ENV ]
then
	echo sourcing environment from ./$LOCAL_ENV
	. ./$LOCAL_ENV
else
	echo $LOCAL_ENV does not exist. Writing deafults to $LOCAL_ENV
	CREATE_ENV=true
fi

CONT=${CONT:='claraparabricks/single-cell-examples_rapids_cuda10.2:latest'}
JUPYTER_PORT=${JUPYTER_PORT:-8888}
PLOTLY_PORT=${PLOTLY_PORT:-5000}
DASK_PORT=${DASK_PORT:-9001}
PROJECT_PATH=${PROJECT_PATH:=$(pwd)}
DATA_PATH=${DATA_PATH:=/workspace/rapids-single-cell-examples/data}

if [ ${CREATE_ENV} = true ]; then
	echo CONT=${CONT} >> $LOCAL_ENV
	echo JUPYTER_PORT=${JUPYTER_PORT} >> $LOCAL_ENV
	echo PLOTLY_PORT=${PLOTLY_PORT} >> $LOCAL_ENV
	echo DASK_PORT=${DASK_PORT} >> $LOCAL_ENV
	echo PROJECT_PATH=${PROJECT_PATH} >> $LOCAL_ENV
	echo DATA_PATH=${DATA_PATH} >> $LOCAL_ENV
fi

DOCKER_CMD="docker run --gpus all --user $(id -u):$(id -g) -p ${JUPYTER_PORT}:8888 -p ${DASK_PORT}:${DASK_PORT} -p ${PLOTLY_PORT}:5000 -v ${DATA_PATH}:/workspace/rapids-single-cell-examples/data --shm-size=1g --ulimit memlock=-1 --ulimit stack=67108864 -e HOME=/workspace/rapids-single-cell-examples/data -e TF_CPP_MIN_LOG_LEVEL=3 -w /workspace/rapids-single-cell-examples"
JUPYTER_CMD="/opt/conda/envs/rapids/bin/jupyter-lab \
		--no-browser \
		--port=8888 \
		--ip=0.0.0.0 \
		--notebook-dir=/workspace \
		--NotebookApp.password=\"\" \
		--NotebookApp.token=\"\" \
		--NotebookApp.password_required=False"

build() {
	echo 'Building container...'
	./build.sh
	exit
}


bash() {
	${DOCKER_CMD} -it ${CONT} bash
	exit
}


setup() {
	local DATA_DIR=${DATA_PATH}/data
	
	if [ ! -d "$DATA_DIR" ]; then
		echo "Downloading datasets..."
		mkdir -p ${DATA_DIR}

		echo 'Downloading 70k krasnow_hlca_10x dataset...'
		wget -q --show-progress \
			-p ${DATA_DIR} \
			https://rapids-single-cell-examples.s3.us-east-2.amazonaws.com/krasnow_hlca_10x.sparse.h5ad

		echo 'Downloading dsci dataset...'
		wget -q --show-progress \
			-p ${DATA_DIR} \
			https://rapids-single-cell-examples.s3.us-east-2.amazonaws.com/dsci_resting_nonzeropeaks.h5ad; \

		wget -q --show-progress \
			-p ${DATA_DIR} \
			https://rapids-single-cell-examples.s3.us-east-2.amazonaws.com/dsci_resting_peaknames_nonzero.npy; \

		wget -q --show-progress \
			-p ${DATA_DIR} \
			https://rapids-single-cell-examples.s3.us-east-2.amazonaws.com/dsci_resting_cell_metadata.csv

		echo 'Downloading 1M brain_cells_10X dataset...'
		wget -q --show-progress \
			-p ${DATA_DIR} \
			https://rapids-single-cell-examples.s3.us-east-2.amazonaws.com/1M_brain_cells_10X.sparse.h5ad
	fi
}

container() {
	${DOCKER_CMD} -it ${CONT} ${JUPYTER_CMD}
	exit
}


jupyter() {
	${JUPYTER_CMD} --allow-root
	exit
}


case $1 in
	build)
		;&
	bash)
		;&
	setup)
		;&
	container)
		$1
		;;
	jupyter)
		$1
		;;
	*)
	usage
		;;
esac