File size: 2,186 Bytes
d149fb1 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 | #!/bin/bash
#
# Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# 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 aria2c &> /dev/null ; then
echo "Error: aria2c could not be found. Please install aria2c (sudo apt install aria2)."
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 "$0")")"
if [[ "${DOWNLOAD_MODE}" = full_dbs ]] ; then
echo "Downloading BFD..."
bash "${SCRIPT_DIR}/download_bfd.sh" "${DOWNLOAD_DIR}"
else
echo "Downloading Small BFD..."
bash "${SCRIPT_DIR}/download_small_bfd.sh" "${DOWNLOAD_DIR}"
fi
echo "Downloading MGnify..."
bash "${SCRIPT_DIR}/download_mgnify.sh" "${DOWNLOAD_DIR}"
echo "Downloading PDB70..."
bash "${SCRIPT_DIR}/download_pdb70.sh" "${DOWNLOAD_DIR}"
echo "Downloading PDB mmCIF files..."
bash "${SCRIPT_DIR}/download_pdb_mmcif.sh" "${DOWNLOAD_DIR}"
echo "Downloading Uniref30..."
bash "${SCRIPT_DIR}/download_uniref30.sh" "${DOWNLOAD_DIR}"
echo "Downloading Uniref90..."
bash "${SCRIPT_DIR}/download_uniref90.sh" "${DOWNLOAD_DIR}"
echo "Downloading UniProt..."
bash "${SCRIPT_DIR}/download_uniprot.sh" "${DOWNLOAD_DIR}"
echo "Downloading PDB SeqRes..."
bash "${SCRIPT_DIR}/download_pdb_seqres.sh" "${DOWNLOAD_DIR}"
echo "All data downloaded."
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