view docker/alphafold/scripts/download_pdb_mmcif.sh @ 1:6c92e000d684 draft

"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"

#!/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, unzips and flattens the PDB database for AlphaFold.
#
# Usage: bash download_pdb_mmcif.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

if ! command -v rsync &> /dev/null ; then
    echo "Error: rsync could not be found. Please install rsync."
    exit 1
fi

DOWNLOAD_DIR="$1"
ROOT_DIR="${DOWNLOAD_DIR}/pdb_mmcif"
RAW_DIR="${ROOT_DIR}/raw"
MMCIF_DIR="${ROOT_DIR}/mmcif_files"

echo "Running rsync to fetch all mmCIF files (note that the rsync progress estimate might be inaccurate)..."
mkdir --parents "${RAW_DIR}"
rsync --recursive --links --perms --times --compress --info=progress2 --delete --port=33444 \
  rsync.rcsb.org::ftp_data/structures/divided/mmCIF/ \
  "${RAW_DIR}"

echo "Unzipping all mmCIF files..."
find "${RAW_DIR}/" -type f -iname "*.gz" -exec gunzip {} +

echo "Flattening all mmCIF files..."
mkdir --parents "${MMCIF_DIR}"
find "${RAW_DIR}" -type d -empty -delete  # Delete empty directories.
for subdir in "${RAW_DIR}"/*; do
  mv "${subdir}/"*.cif "${MMCIF_DIR}"
done

# Delete empty download directory structure.
find "${RAW_DIR}" -type d -empty -delete

aria2c "ftp://ftp.wwpdb.org/pub/pdb/data/status/obsolete.dat" --dir="${ROOT_DIR}"