Mercurial > repos > galaxy-australia > alphafold2
diff scripts/download_pdb70.sh @ 0:7ae9d78b06f5 draft
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
author | galaxy-australia |
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date | Fri, 28 Jan 2022 04:56:29 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/download_pdb70.sh Fri Jan 28 04:56:29 2022 +0000 @@ -0,0 +1,41 @@ +#!/bin/bash +# +# Copyright 2021 DeepMind Technologies Limited +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# +# Downloads and unzips the PDB70 database for AlphaFold. +# +# Usage: bash download_pdb70.sh /path/to/download/directory +set -e + +if [[ $# -eq 0 ]]; then + echo "Error: download directory must be provided as an input argument." + exit 1 +fi + +if ! command -v aria2c &> /dev/null ; then + echo "Error: aria2c could not be found. Please install aria2c (sudo apt install aria2)." + exit 1 +fi + +DOWNLOAD_DIR="$1" +ROOT_DIR="${DOWNLOAD_DIR}/pdb70" +SOURCE_URL="http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/pdb70_from_mmcif_200401.tar.gz" +BASENAME=$(basename "${SOURCE_URL}") + +mkdir --parents "${ROOT_DIR}" +aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}" +tar --extract --verbose --file="${ROOT_DIR}/${BASENAME}" \ + --directory="${ROOT_DIR}" +rm "${ROOT_DIR}/${BASENAME}"