#!/bin/bash # # Original Copyright 2021 DeepMind Technologies Limited # Modifications Copyright 2022 Amazon.com, Inc. or its affiliates. All Rights Reserved. # SPDX-License-Identifier: Apache-2.0 # # Downloads and unzips all required data for AlphaFold. # # Usage: bash download_all_data.sh /path/to/download/directory set -e if [[ $# -eq 0 ]]; then echo "Error: download directory must be provided as an input argument." exit 1 fi if ! command -v aws &> /dev/null ; then echo "Error: awscli could not be found. Please install awscli." exit 1 fi DOWNLOAD_DIR="$1" DOWNLOAD_MODE="${2:-full_dbs}" # Default mode to full_dbs. if [[ "${DOWNLOAD_MODE}" != full_dbs && "${DOWNLOAD_MODE}" != reduced_dbs ]] then echo "DOWNLOAD_MODE ${DOWNLOAD_MODE} not recognized." exit 1 fi SCRIPT_DIR="$(dirname "$(realpath "$0")")" echo "Downloading AlphaFold parameters..." bash "${SCRIPT_DIR}/download_alphafold_params_s3.sh" "${DOWNLOAD_DIR}" if [[ "${DOWNLOAD_MODE}" = reduced_dbs ]] ; then echo "Downloading Small BFD..." bash "${SCRIPT_DIR}/download_small_bfd_s3.sh" "${DOWNLOAD_DIR}" else echo "Downloading BFD..." bash "${SCRIPT_DIR}/download_bfd_s3.sh" "${DOWNLOAD_DIR}" fi echo "Downloading MGnify..." bash "${SCRIPT_DIR}/download_mgnify_s3.sh" "${DOWNLOAD_DIR}" echo "Downloading PDB70..." bash "${SCRIPT_DIR}/download_pdb70_s3.sh" "${DOWNLOAD_DIR}" echo "Downloading PDB mmCIF files..." bash "${SCRIPT_DIR}/download_pdb_mmcif_s3.sh" "${DOWNLOAD_DIR}" echo "Downloading Uniclust30..." bash "${SCRIPT_DIR}/download_uniclust30_s3.sh" "${DOWNLOAD_DIR}" echo "Downloading Uniref90..." bash "${SCRIPT_DIR}/download_uniref90_s3.sh" "${DOWNLOAD_DIR}" echo "Downloading UniProt..." bash "${SCRIPT_DIR}/download_uniprot_s3.sh" "${DOWNLOAD_DIR}" echo "Downloading PDB SeqRes..." bash "${SCRIPT_DIR}/download_pdb_seqres_s3.sh" "${DOWNLOAD_DIR}" echo "All data downloaded."