Add database setup script from https://github.com/sokrypton/ColabFold…

…/blob/main/setup_databases.sh

setup_databases.sh

@@ -0,0 +1,87 @@
+#!/bin/bash -ex
+# Setup everything for using mmseqs locally
+ARIA_NUM_CONN=8
+WORKDIR="${1:-$(pwd)}"
+
+PDB_SERVER="${2:-"rsync.wwpdb.org::ftp"}"
+PDB_PORT="${3:-"33444"}"
+
+cd "${WORKDIR}"
+
+hasCommand () {
+    command -v "$1" >/dev/null 2>&1
+}
+
+STRATEGY=""
+if hasCommand aria2c; then STRATEGY="$STRATEGY ARIA"; fi
+if hasCommand curl;   then STRATEGY="$STRATEGY CURL"; fi
+if hasCommand wget;   then STRATEGY="$STRATEGY WGET"; fi
+if [ "$STRATEGY" = "" ]; then
+	    fail "No download tool found in PATH. Please install aria2c, curl or wget."
+fi
+
+downloadFile() {
+    URL="$1"
+    OUTPUT="$2"
+    set +e
+    for i in $STRATEGY; do
+        case "$i" in
+        ARIA)
+            FILENAME=$(basename "${OUTPUT}")
+            DIR=$(dirname "${OUTPUT}")
+            aria2c --max-connection-per-server="$ARIA_NUM_CONN" --allow-overwrite=true -o "$FILENAME" -d "$DIR" "$URL" && set -e && return 0
+            ;;
+        CURL)
+            curl -L -o "$OUTPUT" "$URL" && set -e && return 0
+            ;;
+        WGET)
+            wget -O "$OUTPUT" "$URL" && set -e && return 0
+            ;;
+        esac
+    done
+    set -e
+    fail "Could not download $URL to $OUTPUT"
+}
+
+if [ ! -f UNIREF30_READY ]; then
+  downloadFile "https://wwwuser.gwdg.de/~compbiol/colabfold/uniref30_2202.tar.gz" "uniref30_2202.tar.gz"
+  tar xzvf "uniref30_2202.tar.gz"
+  mmseqs tsv2exprofiledb "uniref30_2202" "uniref30_2202_db"
+  mmseqs createindex "uniref30_2202_db" tmp1 --remove-tmp-files 1
+  if [ -e uniref30_2202_db_mapping ]; then
+    ln -sf uniref30_2202_db_mapping uniref30_2202_db.idx_mapping
+  fi
+  if [ -e uniref30_2202_db_taxonomy ]; then
+    ln -sf uniref30_2202_db_taxonomy uniref30_2202_db.idx_taxonomy
+  fi
+  touch UNIREF30_READY
+fi
+
+if [ ! -f COLABDB_READY ]; then
+  downloadFile "https://wwwuser.gwdg.de/~compbiol/colabfold/colabfold_envdb_202108.tar.gz" "colabfold_envdb_202108.tar.gz"
+  tar xzvf "colabfold_envdb_202108.tar.gz"
+  mmseqs tsv2exprofiledb "colabfold_envdb_202108" "colabfold_envdb_202108_db"
+  # TODO: split memory value for createindex?
+  mmseqs createindex "colabfold_envdb_202108_db" tmp2 --remove-tmp-files 1
+  touch COLABDB_READY
+fi
+
+if [ ! -f PDB_READY ]; then
+  downloadFile "https://wwwuser.gwdg.de/~compbiol/colabfold/pdb70_220313.fasta.gz" "pdb70_220313.fasta.gz"
+  mmseqs createdb pdb70_220313.fasta.gz pdb70_220313
+  mmseqs createindex pdb70_220313 tmp3 --remove-tmp-files 1
+  touch PDB_READY
+fi
+
+if [ ! -f PDB70_READY ]; then
+  downloadFile "https://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/pdb70_from_mmcif_220313.tar.gz" "pdb70_from_mmcif_220313.tar.gz"
+  tar xzvf pdb70_from_mmcif_220313.tar.gz pdb70_a3m.ffdata pdb70_a3m.ffindex
+  touch PDB70_READY
+fi
+if [ ! -f PDB_MMCIF_READY ]; then
+  mkdir -p pdb/divided
+  mkdir -p pdb/obsolete
+  rsync -rlpt -v -z --delete --port=${PDB_PORT} ${PDB_SERVER}/data/structures/divided/mmCIF/ pdb/divided
+  rsync -rlpt -v -z --delete --port=${PDB_PORT} ${PDB_SERVER}/data/structures/obsolete/mmCIF/ pdb/obsolete
+  touch PDB_MMCIF_READY
+fi