Added the shell script to download the BFD database for HHBlits queries.

scripts/download_bfd.sh

+#!/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 BFD database for AlphaFold.
+#
+# Usage: bash download_bfd.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}/bfd"
+# Mirror of:
+# https://bfd.mmseqs.com/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz.
+SOURCE_URL="https://storage.googleapis.com/alphafold-databases/casp14_versions/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.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}"