Mercurial > repos > galaxy-australia > alphafold2

annotate scripts/download_all_data.sh @ 1:6c92e000d684 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
author galaxy-australia
date Tue, 01 Mar 2022 02:53:05 +0000
parents 7ae9d78b06f5
children
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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
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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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 and unzips all required data for AlphaFold.
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18 #
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19 # Usage: bash download_all_data.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 DOWNLOAD_DIR="$1"
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33 DOWNLOAD_MODE="${2:-full_dbs}" # Default mode to full_dbs.
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34 if [[ "${DOWNLOAD_MODE}" != full_dbs && "${DOWNLOAD_MODE}" != reduced_dbs ]]
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35 then
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36 echo "DOWNLOAD_MODE ${DOWNLOAD_MODE} not recognized."
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37 exit 1
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38 fi
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39
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40 SCRIPT_DIR="$(dirname "$(realpath "$0")")"
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41
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42 echo "Downloading AlphaFold parameters..."
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43 bash "${SCRIPT_DIR}/download_alphafold_params.sh" "${DOWNLOAD_DIR}"
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44
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45 if [[ "${DOWNLOAD_MODE}" = reduced_dbs ]] ; then
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46 echo "Downloading Small BFD..."
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47 bash "${SCRIPT_DIR}/download_small_bfd.sh" "${DOWNLOAD_DIR}"
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48 else
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49 echo "Downloading BFD..."
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50 bash "${SCRIPT_DIR}/download_bfd.sh" "${DOWNLOAD_DIR}"
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51 fi
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52
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53 echo "Downloading MGnify..."
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54 bash "${SCRIPT_DIR}/download_mgnify.sh" "${DOWNLOAD_DIR}"
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55
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56 echo "Downloading PDB70..."
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57 bash "${SCRIPT_DIR}/download_pdb70.sh" "${DOWNLOAD_DIR}"
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58
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59 echo "Downloading PDB mmCIF files..."
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60 bash "${SCRIPT_DIR}/download_pdb_mmcif.sh" "${DOWNLOAD_DIR}"
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61
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62 echo "Downloading Uniclust30..."
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63 bash "${SCRIPT_DIR}/download_uniclust30.sh" "${DOWNLOAD_DIR}"
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64
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65 echo "Downloading Uniref90..."
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66 bash "${SCRIPT_DIR}/download_uniref90.sh" "${DOWNLOAD_DIR}"
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67
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68 echo "Downloading UniProt..."
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69 bash "${SCRIPT_DIR}/download_uniprot.sh" "${DOWNLOAD_DIR}"
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70
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71 echo "Downloading PDB SeqRes..."
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72 bash "${SCRIPT_DIR}/download_pdb_seqres.sh" "${DOWNLOAD_DIR}"
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73
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74 echo "All data downloaded."