Mercurial > repos > galaxy-australia > alphafold2

comparison scripts/download_pdb70.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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-1:000000000000 0:7ae9d78b06f5
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 PDB70 database for AlphaFold.
18 #
19 # Usage: bash download_pdb70.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}/pdb70"
34 SOURCE_URL="http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/pdb70_from_mmcif_200401.tar.gz"
35 BASENAME=$(basename "${SOURCE_URL}")
36
37 mkdir --parents "${ROOT_DIR}"
38 aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
39 tar --extract --verbose --file="${ROOT_DIR}/${BASENAME}" \
40 --directory="${ROOT_DIR}"
41 rm "${ROOT_DIR}/${BASENAME}"