Mercurial > repos > galaxy-australia > alphafold2
comparison scripts/download_uniprot.sh @ 0:7ae9d78b06f5 draft
"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 |
| parents | |
| children |
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| -1:000000000000 | 0:7ae9d78b06f5 |
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| 1 #!/bin/bash | |
| 2 # | |
| 3 # Copyright 2021 DeepMind Technologies Limited | |
| 4 # | |
| 5 # Licensed under the Apache License, Version 2.0 (the "License"); | |
| 6 # you may not use this file except in compliance with the License. | |
| 7 # You may obtain a copy of the License at | |
| 8 # | |
| 9 # http://www.apache.org/licenses/LICENSE-2.0 | |
| 10 # | |
| 11 # Unless required by applicable law or agreed to in writing, software | |
| 12 # distributed under the License is distributed on an "AS IS" BASIS, | |
| 13 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | |
| 14 # See the License for the specific language governing permissions and | |
| 15 # limitations under the License. | |
| 16 # | |
| 17 # Downloads, unzips and merges the SwissProt and TrEMBL databases for | |
| 18 # AlphaFold-Multimer. | |
| 19 # | |
| 20 # Usage: bash download_uniprot.sh /path/to/download/directory | |
| 21 set -e | |
| 22 | |
| 23 if [[ $# -eq 0 ]]; then | |
| 24 echo "Error: download directory must be provided as an input argument." | |
| 25 exit 1 | |
| 26 fi | |
| 27 | |
| 28 if ! command -v aria2c &> /dev/null ; then | |
| 29 echo "Error: aria2c could not be found. Please install aria2c (sudo apt install aria2)." | |
| 30 exit 1 | |
| 31 fi | |
| 32 | |
| 33 DOWNLOAD_DIR="$1" | |
| 34 ROOT_DIR="${DOWNLOAD_DIR}/uniprot" | |
| 35 | |
| 36 TREMBL_SOURCE_URL="ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz" | |
| 37 TREMBL_BASENAME=$(basename "${TREMBL_SOURCE_URL}") | |
| 38 TREMBL_UNZIPPED_BASENAME="${TREMBL_BASENAME%.gz}" | |
| 39 | |
| 40 SPROT_SOURCE_URL="ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz" | |
| 41 SPROT_BASENAME=$(basename "${SPROT_SOURCE_URL}") | |
| 42 SPROT_UNZIPPED_BASENAME="${SPROT_BASENAME%.gz}" | |
| 43 | |
| 44 mkdir --parents "${ROOT_DIR}" | |
| 45 aria2c "${TREMBL_SOURCE_URL}" --dir="${ROOT_DIR}" | |
| 46 aria2c "${SPROT_SOURCE_URL}" --dir="${ROOT_DIR}" | |
| 47 pushd "${ROOT_DIR}" | |
| 48 gunzip "${ROOT_DIR}/${TREMBL_BASENAME}" | |
| 49 gunzip "${ROOT_DIR}/${SPROT_BASENAME}" | |
| 50 | |
| 51 # Concatenate TrEMBL and SwissProt, rename to uniprot and clean up. | |
| 52 cat "${ROOT_DIR}/${SPROT_UNZIPPED_BASENAME}" >> "${ROOT_DIR}/${TREMBL_UNZIPPED_BASENAME}" | |
| 53 mv "${ROOT_DIR}/${TREMBL_UNZIPPED_BASENAME}" "${ROOT_DIR}/uniprot.fasta" | |
| 54 rm "${ROOT_DIR}/${SPROT_UNZIPPED_BASENAME}" | |
| 55 popd |