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annotate scripts/download_uniprot.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 merges the SwissProt and TrEMBL databases for
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18 # AlphaFold-Multimer.
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19 #
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20 # Usage: bash download_uniprot.sh /path/to/download/directory
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21 set -e
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23 if [[ $# -eq 0 ]]; then
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24 echo "Error: download directory must be provided as an input argument."
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25 exit 1
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26 fi
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28 if ! command -v aria2c &> /dev/null ; then
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29 echo "Error: aria2c could not be found. Please install aria2c (sudo apt install aria2)."
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30 exit 1
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31 fi
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33 DOWNLOAD_DIR="$1"
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34 ROOT_DIR="${DOWNLOAD_DIR}/uniprot"
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36 TREMBL_SOURCE_URL="ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz"
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37 TREMBL_BASENAME=$(basename "${TREMBL_SOURCE_URL}")
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38 TREMBL_UNZIPPED_BASENAME="${TREMBL_BASENAME%.gz}"
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40 SPROT_SOURCE_URL="ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz"
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41 SPROT_BASENAME=$(basename "${SPROT_SOURCE_URL}")
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42 SPROT_UNZIPPED_BASENAME="${SPROT_BASENAME%.gz}"
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44 mkdir --parents "${ROOT_DIR}"
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45 aria2c "${TREMBL_SOURCE_URL}" --dir="${ROOT_DIR}"
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46 aria2c "${SPROT_SOURCE_URL}" --dir="${ROOT_DIR}"
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47 pushd "${ROOT_DIR}"
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48 gunzip "${ROOT_DIR}/${TREMBL_BASENAME}"
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49 gunzip "${ROOT_DIR}/${SPROT_BASENAME}"
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50
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51 # Concatenate TrEMBL and SwissProt, rename to uniprot and clean up.
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52 cat "${ROOT_DIR}/${SPROT_UNZIPPED_BASENAME}" >> "${ROOT_DIR}/${TREMBL_UNZIPPED_BASENAME}"
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53 mv "${ROOT_DIR}/${TREMBL_UNZIPPED_BASENAME}" "${ROOT_DIR}/uniprot.fasta"
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54 rm "${ROOT_DIR}/${SPROT_UNZIPPED_BASENAME}"
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55 popd