[Shell] Install BWA, Samtools, Bcftools, and Bedtools

install_bio_stack.sh

#!/usr/bin/env bash
#
# Usage:  ./install_bio_stack.sh <dest dir path>

set -uex
PREFIX_DIR=$(realpath "${1}")
BIN_DIR="${PREFIX_DIR}/bin"
SRC_DIR="${PREFIX_DIR}/src"

mkdir -p "${SRC_DIR}" "${BIN_DIR}"

function clone-or-pull {
  for r in "${@}"; do
    dest="${SRC_DIR}/${r##*/}"
    if [[ -d "${dest}" ]]; then
      cd "${dest}" && git pull
    else
      git clone "https://github.com/${r}.git" "${dest}"
    fi
  done
}

clone-or-pull \
  lh3/bwa \
  samtools/htslib \
  samtools/samtools \
  samtools/bcftools \
  arq5x/bedtools2

cd "${SRC_DIR}/bwa" \
  && make \
  && cd "${BIN_DIR}" \
  && find ../src/bwa -maxdepth 1 -type f -executable \
    -exec cp -f {} "${BIN_DIR}" \;

cd "${SRC_DIR}/htslib" \
  && autoheader \
  && autoconf \
  && ./configure --prefix="${PREFIX_DIR}" \
  && make \
  && make install

cd "${SRC_DIR}/samtools" \
  && autoheader \
  && autoconf \
  && ./configure --prefix="${PREFIX_DIR}" \
  && make \
  && make install

cd "${SRC_DIR}/bcftools" \
  && autoheader \
  && autoconf \
  && ./configure --prefix="${PREFIX_DIR}" \
  && make \
  && make install

cd "${SRC_DIR}/bedtools2" \
  && make \
  && cp -f "${SRC_DIR}/bedtools2/bin/"* "${BIN_DIR}"