diff docker/alphafold/scripts/download_pdb_mmcif.sh @ 1:6c92e000d684 draft

"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docker/alphafold/scripts/download_pdb_mmcif.sh	Tue Mar 01 02:53:05 2022 +0000
@@ -0,0 +1,61 @@
+#!/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, unzips and flattens the PDB database for AlphaFold.
+#
+# Usage: bash download_pdb_mmcif.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
+
+if ! command -v rsync &> /dev/null ; then
+    echo "Error: rsync could not be found. Please install rsync."
+    exit 1
+fi
+
+DOWNLOAD_DIR="$1"
+ROOT_DIR="${DOWNLOAD_DIR}/pdb_mmcif"
+RAW_DIR="${ROOT_DIR}/raw"
+MMCIF_DIR="${ROOT_DIR}/mmcif_files"
+
+echo "Running rsync to fetch all mmCIF files (note that the rsync progress estimate might be inaccurate)..."
+mkdir --parents "${RAW_DIR}"
+rsync --recursive --links --perms --times --compress --info=progress2 --delete --port=33444 \
+  rsync.rcsb.org::ftp_data/structures/divided/mmCIF/ \
+  "${RAW_DIR}"
+
+echo "Unzipping all mmCIF files..."
+find "${RAW_DIR}/" -type f -iname "*.gz" -exec gunzip {} +
+
+echo "Flattening all mmCIF files..."
+mkdir --parents "${MMCIF_DIR}"
+find "${RAW_DIR}" -type d -empty -delete  # Delete empty directories.
+for subdir in "${RAW_DIR}"/*; do
+  mv "${subdir}/"*.cif "${MMCIF_DIR}"
+done
+
+# Delete empty download directory structure.
+find "${RAW_DIR}" -type d -empty -delete
+
+aria2c "ftp://ftp.wwpdb.org/pub/pdb/data/status/obsolete.dat" --dir="${ROOT_DIR}"