run_wgs_case_study_docker.sh

#!/bin/bash
# Copyright 2018 Google LLC.

set -euo pipefail

## Preliminaries
# Set a number of shell variables, to make what follows easier to read.
BASE="${HOME}/case-study"
BIN_VERSION="1.0.0"

INPUT_DIR="${BASE}/input/data"
REF="GCA_000001405.15_GRCh38_no_alt_analysis_set.fna"
BAM="HG002.novaseq.pcr-free.35x.dedup.grch38_no_alt.bam"
TRUTH_VCF="HG002_GRCh38_1_22_v4.2_benchmark.vcf.gz"
TRUTH_BED="HG002_GRCh38_1_22_v4.2_benchmark.bed"

N_SHARDS="64"

OUTPUT_DIR="${BASE}/output"
OUTPUT_VCF="HG002.output.vcf.gz"
OUTPUT_GVCF="HG002.output.g.vcf.gz"
LOG_DIR="${OUTPUT_DIR}/logs"

## Create local directory structure
mkdir -p "${OUTPUT_DIR}"
mkdir -p "${INPUT_DIR}"
mkdir -p "${LOG_DIR}"


## Download extra packages
# Install aria2 to download data files.
sudo apt-get -qq -y update
sudo apt-get -qq -y install aria2

if ! hash docker 2>/dev/null; then
  echo "'docker' was not found in PATH. Installing docker..."
  # Install docker using instructions on:
  # https://docs.docker.com/install/linux/docker-ce/ubuntu/
  sudo apt-get -qq -y install \
    apt-transport-https \
    ca-certificates \
    curl \
    gnupg-agent \
    software-properties-common
  curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
  sudo add-apt-repository \
    "deb [arch=amd64] https://download.docker.com/linux/ubuntu \
    $(lsb_release -cs) \
    stable"
  sudo apt-get -qq -y update
  sudo apt-get -qq -y install docker-ce
fi


# Copy the data, using http:// because of https://github.com/aria2/aria2/issues/1012.
aria2c -c -x10 -s10 "http://storage.googleapis.com/deepvariant/case-study-testdata/${TRUTH_BED}" -d "${INPUT_DIR}"
aria2c -c -x10 -s10 "http://storage.googleapis.com/deepvariant/case-study-testdata/${TRUTH_VCF}" -d "${INPUT_DIR}"
aria2c -c -x10 -s10 "http://storage.googleapis.com/deepvariant/case-study-testdata/${TRUTH_VCF}.tbi" -d "${INPUT_DIR}"
aria2c -c -x10 -s10 "http://storage.googleapis.com/deepvariant/case-study-testdata/${BAM}" -d "${INPUT_DIR}"
aria2c -c -x10 -s10 "http://storage.googleapis.com/deepvariant/case-study-testdata/${BAM}.bai" -d "${INPUT_DIR}"
aria2c -c -x10 -s10 "http://storage.googleapis.com/deepvariant/case-study-testdata/${REF}.gz" -d "${INPUT_DIR}"
aria2c -c -x10 -s10 "http://storage.googleapis.com/deepvariant/case-study-testdata/${REF}.gz.fai" -d "${INPUT_DIR}"
aria2c -c -x10 -s10 "http://storage.googleapis.com/deepvariant/case-study-testdata/${REF}.gz.gzi" -d "${INPUT_DIR}"
aria2c -c -x10 -s10 "http://storage.googleapis.com/deepvariant/case-study-testdata/${REF}.gzi" -d "${INPUT_DIR}"
aria2c -c -x10 -s10 "http://storage.googleapis.com/deepvariant/case-study-testdata/${REF}.fai" -d "${INPUT_DIR}"

## Pull the docker image.
sudo docker pull google/deepvariant:"${BIN_VERSION}"

echo "Run DeepVariant..."
sudo docker run \
  -v "${INPUT_DIR}":"/input" \
  -v "${OUTPUT_DIR}:/output" \
  google/deepvariant:"${BIN_VERSION}" \
  /opt/deepvariant/bin/run_deepvariant \
  --model_type=WGS \
  --ref="/input/${REF}.gz" \
  --reads="/input/${BAM}" \
  --output_vcf=/output/${OUTPUT_VCF} \
  --output_gvcf=/output/${OUTPUT_GVCF} \
  --num_shards=${N_SHARDS}
echo "Done."
echo

## Evaluation: run hap.py
echo "Start evaluation with hap.py..."
UNCOMPRESSED_REF="${INPUT_DIR}/${REF}"

# hap.py cannot read the compressed fa, so uncompress
# into a writable directory. Index file was downloaded earlier.
zcat <"${INPUT_DIR}/${REF}.gz" >"${UNCOMPRESSED_REF}"

sudo docker pull pkrusche/hap.py
( sudo docker run -i \
-v "${INPUT_DIR}:${INPUT_DIR}" \
-v "${OUTPUT_DIR}:${OUTPUT_DIR}" \
pkrusche/hap.py /opt/hap.py/bin/hap.py \
  "${INPUT_DIR}/${TRUTH_VCF}" \
  "${OUTPUT_DIR}/${OUTPUT_VCF}" \
  -f "${INPUT_DIR}/${TRUTH_BED}" \
  -r "${UNCOMPRESSED_REF}" \
  -o "${OUTPUT_DIR}/happy.output" \
  --engine=vcfeval
) 2>&1 | tee "${LOG_DIR}/happy.log"
echo "Done."