Mercurial > repos > galaxy-australia > alphafold2

annotate scripts/download_pdb_mmcif.sh @ 0:7ae9d78b06f5 draft

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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
author galaxy-australia
date Fri, 28 Jan 2022 04:56:29 +0000
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7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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1 #!/bin/bash
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2 #
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3 # Copyright 2021 DeepMind Technologies Limited
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4 #
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5 # Licensed under the Apache License, Version 2.0 (the "License");
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6 # you may not use this file except in compliance with the License.
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7 # You may obtain a copy of the License at
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8 #
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9 # http://www.apache.org/licenses/LICENSE-2.0
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10 #
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11 # Unless required by applicable law or agreed to in writing, software
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12 # distributed under the License is distributed on an "AS IS" BASIS,
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13 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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14 # See the License for the specific language governing permissions and
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15 # limitations under the License.
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16 #
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17 # Downloads, unzips and flattens the PDB database for AlphaFold.
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18 #
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19 # Usage: bash download_pdb_mmcif.sh /path/to/download/directory
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20 set -e
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21
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22 if [[ $# -eq 0 ]]; then
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23 echo "Error: download directory must be provided as an input argument."
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24 exit 1
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25 fi
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26
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27 if ! command -v aria2c &> /dev/null ; then
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28 echo "Error: aria2c could not be found. Please install aria2c (sudo apt install aria2)."
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29 exit 1
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30 fi
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31
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32 if ! command -v rsync &> /dev/null ; then
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33 echo "Error: rsync could not be found. Please install rsync."
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34 exit 1
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35 fi
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36
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37 DOWNLOAD_DIR="$1"
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38 ROOT_DIR="${DOWNLOAD_DIR}/pdb_mmcif"
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39 RAW_DIR="${ROOT_DIR}/raw"
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40 MMCIF_DIR="${ROOT_DIR}/mmcif_files"
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41
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42 echo "Running rsync to fetch all mmCIF files (note that the rsync progress estimate might be inaccurate)..."
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43 mkdir --parents "${RAW_DIR}"
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44 rsync --recursive --links --perms --times --compress --info=progress2 --delete --port=33444 \
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45 rsync.rcsb.org::ftp_data/structures/divided/mmCIF/ \
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46 "${RAW_DIR}"
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47
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48 echo "Unzipping all mmCIF files..."
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49 find "${RAW_DIR}/" -type f -iname "*.gz" -exec gunzip {} +
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50
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51 echo "Flattening all mmCIF files..."
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52 mkdir --parents "${MMCIF_DIR}"
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53 find "${RAW_DIR}" -type d -empty -delete # Delete empty directories.
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54 for subdir in "${RAW_DIR}"/*; do
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55 mv "${subdir}/"*.cif "${MMCIF_DIR}"
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56 done
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57
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58 # Delete empty download directory structure.
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59 find "${RAW_DIR}" -type d -empty -delete
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60
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61 aria2c "ftp://ftp.wwpdb.org/pub/pdb/data/status/obsolete.dat" --dir="${ROOT_DIR}"