Add script to download embeddings for training SoloSeq

scripts/download_soloseq_embeddings.sh

@@ -0,0 +1,34 @@
+#!/bin/bash
+#
+# Copyright 2024 AlQuraishi Laboratory
+#
+# 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 ESM-1b embeddings used to train OpenFold SoloSeq single-seq model.
+#
+# Usage: bash download_soloseq_embeddings.sh /path/to/download/directory
+set -e
+
+if [[ $# -eq 0 ]]; then
+    echo "Error: download directory must be provided as an input argument."
+    exit 1
+fi
+
+if ! command -v aws &> /dev/null ; then
+    echo "Error: aws could not be found. Please install aws."
+    exit 1
+fi
+
+DOWNLOAD_DIR="${1}/soloseq_embeddings"
+mkdir -p "${DOWNLOAD_DIR}"
+aws s3 cp --no-sign-request --region us-east-1 s3://openfold/soloseq_embeddings/ "${DOWNLOAD_DIR}" --recursive