Mercurial > repos > galaxy-australia > alphafold2

annotate scripts/download_pdb70.sh @ 1:6c92e000d684 draft

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"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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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 and unzips the PDB70 database for AlphaFold.
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18 #
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19 # Usage: bash download_pdb70.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="$1"
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33 ROOT_DIR="${DOWNLOAD_DIR}/pdb70"
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34 SOURCE_URL="http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/pdb70_from_mmcif_200401.tar.gz"
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35 BASENAME=$(basename "${SOURCE_URL}")
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36
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37 mkdir --parents "${ROOT_DIR}"
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38 aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
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39 tar --extract --verbose --file="${ROOT_DIR}/${BASENAME}" \
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40 --directory="${ROOT_DIR}"
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41 rm "${ROOT_DIR}/${BASENAME}"