Mercurial > repos > galaxy-australia > alphafold2
comparison docker/alphafold/scripts/download_pdb_seqres.sh @ 1:6c92e000d684 draft
"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 |
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| children |
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| 0:7ae9d78b06f5 | 1:6c92e000d684 |
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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 and unzips the PDB SeqRes database for AlphaFold. | |
| 18 # | |
| 19 # Usage: bash download_pdb_seqres.sh /path/to/download/directory | |
| 20 set -e | |
| 21 | |
| 22 if [[ $# -eq 0 ]]; then | |
| 23 echo "Error: download directory must be provided as an input argument." | |
| 24 exit 1 | |
| 25 fi | |
| 26 | |
| 27 if ! command -v aria2c &> /dev/null ; then | |
| 28 echo "Error: aria2c could not be found. Please install aria2c (sudo apt install aria2)." | |
| 29 exit 1 | |
| 30 fi | |
| 31 | |
| 32 DOWNLOAD_DIR="$1" | |
| 33 ROOT_DIR="${DOWNLOAD_DIR}/pdb_seqres" | |
| 34 SOURCE_URL="ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt" | |
| 35 BASENAME=$(basename "${SOURCE_URL}") | |
| 36 | |
| 37 mkdir --parents "${ROOT_DIR}" | |
| 38 aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}" |