Mercurial > repos > galaxy-australia > alphafold2
annotate scripts/download_pdb70.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 |
parents | 7ae9d78b06f5 |
children |
rev | line source |
---|---|
0
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
1 #!/bin/bash |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
2 # |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
3 # Copyright 2021 DeepMind Technologies Limited |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
4 # |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
5 # Licensed under the Apache License, Version 2.0 (the "License"); |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
6 # you may not use this file except in compliance with the License. |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
7 # You may obtain a copy of the License at |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
8 # |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
9 # http://www.apache.org/licenses/LICENSE-2.0 |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
10 # |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
11 # Unless required by applicable law or agreed to in writing, software |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
12 # distributed under the License is distributed on an "AS IS" BASIS, |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
13 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
14 # See the License for the specific language governing permissions and |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
15 # limitations under the License. |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
16 # |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
17 # Downloads and unzips the PDB70 database for AlphaFold. |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
18 # |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
19 # Usage: bash download_pdb70.sh /path/to/download/directory |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
20 set -e |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
21 |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
22 if [[ $# -eq 0 ]]; then |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
23 echo "Error: download directory must be provided as an input argument." |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
24 exit 1 |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
25 fi |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
26 |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
27 if ! command -v aria2c &> /dev/null ; then |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
28 echo "Error: aria2c could not be found. Please install aria2c (sudo apt install aria2)." |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
29 exit 1 |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
30 fi |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
31 |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
32 DOWNLOAD_DIR="$1" |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
33 ROOT_DIR="${DOWNLOAD_DIR}/pdb70" |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
34 SOURCE_URL="http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/pdb70_from_mmcif_200401.tar.gz" |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
35 BASENAME=$(basename "${SOURCE_URL}") |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
36 |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
37 mkdir --parents "${ROOT_DIR}" |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
38 aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}" |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
39 tar --extract --verbose --file="${ROOT_DIR}/${BASENAME}" \ |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
40 --directory="${ROOT_DIR}" |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff
changeset
|
41 rm "${ROOT_DIR}/${BASENAME}" |