diff docker/alphafold/scripts/download_all_data.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_all_data.sh	Tue Mar 01 02:53:05 2022 +0000
@@ -0,0 +1,74 @@
+#!/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 all required data for AlphaFold.
+#
+# Usage: bash download_all_data.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="$1"
+DOWNLOAD_MODE="${2:-full_dbs}"  # Default mode to full_dbs.
+if [[ "${DOWNLOAD_MODE}" != full_dbs && "${DOWNLOAD_MODE}" != reduced_dbs ]]
+then
+  echo "DOWNLOAD_MODE ${DOWNLOAD_MODE} not recognized."
+  exit 1
+fi
+
+SCRIPT_DIR="$(dirname "$(realpath "$0")")"
+
+echo "Downloading AlphaFold parameters..."
+bash "${SCRIPT_DIR}/download_alphafold_params.sh" "${DOWNLOAD_DIR}"
+
+if [[ "${DOWNLOAD_MODE}" = reduced_dbs ]] ; then
+  echo "Downloading Small BFD..."
+  bash "${SCRIPT_DIR}/download_small_bfd.sh" "${DOWNLOAD_DIR}"
+else
+  echo "Downloading BFD..."
+  bash "${SCRIPT_DIR}/download_bfd.sh" "${DOWNLOAD_DIR}"
+fi
+
+echo "Downloading MGnify..."
+bash "${SCRIPT_DIR}/download_mgnify.sh" "${DOWNLOAD_DIR}"
+
+echo "Downloading PDB70..."
+bash "${SCRIPT_DIR}/download_pdb70.sh" "${DOWNLOAD_DIR}"
+
+echo "Downloading PDB mmCIF files..."
+bash "${SCRIPT_DIR}/download_pdb_mmcif.sh" "${DOWNLOAD_DIR}"
+
+echo "Downloading Uniclust30..."
+bash "${SCRIPT_DIR}/download_uniclust30.sh" "${DOWNLOAD_DIR}"
+
+echo "Downloading Uniref90..."
+bash "${SCRIPT_DIR}/download_uniref90.sh" "${DOWNLOAD_DIR}"
+
+echo "Downloading UniProt..."
+bash "${SCRIPT_DIR}/download_uniprot.sh" "${DOWNLOAD_DIR}"
+
+echo "Downloading PDB SeqRes..."
+bash "${SCRIPT_DIR}/download_pdb_seqres.sh" "${DOWNLOAD_DIR}"
+
+echo "All data downloaded."