Thank you for inventing such an excellent tool. Due to network issues, I initially downloaded the required databases (such as afdb_swissprot.tar.gz and afdb_swissprot.version) on Windows from https://foldseek.steineggerlab.workers.dev/. Then, on Linux, I used the command foldseek databases Alphafold/Swiss-Prot afdb_swissprot tmp and placed the downloaded files in the tmp path. However, I noticed that it still attempted to re-download the afdb_swissprot.tar.gz file. Upon checking the download.sh script, I found an error on line 130, where the filename used to check for existence was alphafold_swissprot.tar.gz. Therefore, I manually added the alphafold_swissprot.tar.gz file, allowing the command to run successfully. Similar errors also occurred during the download of afdb_proteome (line 121).

`#!/bin/sh -e fail() { echo "Error: $1" exit 1 }

notExists() { [ ! -f "$1" ] }

hasCommand () { command -v "$1" >/dev/null 2>&1 }

ARR="" push_back() {

shellcheck disable=SC1003

CURR="$(printf '%s' "$1" | awk '{ gsub(/'\''/, "'\''\\'\'''\''"); print; }')"
if [ -z "$ARR" ]; then
    ARR=''\'$CURR\'''
else
    ARR=$ARR' '\'$CURR\'''
fi

}

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" && return 0 ;; CURL) curl -L -o "$OUTPUT" "$URL" && return 0 ;; WGET) wget -O "$OUTPUT" "$URL" && return 0 ;; esac done set -e fail "Could not download $URL to $OUTPUT" }

downloadFileList() { URL="$1" OUTPUT_DIR="$2" INPUT_FILE="$OUTPUT_DIR/input.txt" downloadFile "$URL" "$INPUT_FILE" set +e for i in $STRATEGY; do case "$i" in ARIA) aria2c -c --max-connection-per-server="$ARIA_NUM_CONN" --allow-overwrite=true --dir="$OUTPUT_DIR" --input-file="$INPUT_FILE" && return 0 ;; CURL) (cd "$OUTPUT_DIR"; xargs -n 1 curl -C - -L -O < "$INPUT_FILE") && return 0 ;; WGET) wget --continue -P "$OUTPUT_DIR" --input-file="$INPUT_FILE" && return 0 ;; esac done set -e rm -f "$OUTPUT/input.txt" fail "Could not download $URL to $OUTPUT" }

check number of input variables

[ "$#" -ne 3 ] && echo "Please provide " && exit 1; [ ! -d "$3" ] && echo "tmp directory $3 not found!" && mkdir -p "$3";

SELECTION="$1" OUTDB="$2" TMP_PATH="$3"

INPUT_TYPE="" case "${SELECTION}" in "Alphafold/UniProt") if notExists "${TMP_PATH}/afdb.tar.gz"; then downloadFile "https://foldseek.steineggerlab.workers.dev/afdb.tar.gz" "${TMP_PATH}/afdb.tar.gz" downloadFile "https://foldseek.steineggerlab.workers.dev/afdb.version" "${TMP_PATH}/version" fi tar xvfz "${TMP_PATH}/afdb.tar.gz" -C "${TMP_PATH}" push_back "${TMP_PATH}/afdb" INPUT_TYPE="FOLDSEEK_DB" ;; "Alphafold/UniProt50-minimal") if notExists "${TMP_PATH}/afdb50.tar.gz"; then downloadFile "https://foldseek.steineggerlab.workers.dev/afdb50.tar.gz" "${TMP_PATH}/afdb50.tar.gz" downloadFile "https://foldseek.steineggerlab.workers.dev/afdb50.version" "${TMP_PATH}/version" fi tar xvfz "${TMP_PATH}/afdb50.tar.gz" -C "${TMP_PATH}" push_back "${TMP_PATH}/afdb50" INPUT_TYPE="FOLDSEEK_DB" ;; "Alphafold/UniProt50") if notExists "${TMP_PATH}/afdb50.tar.gz"; then downloadFile "https://foldseek.steineggerlab.workers.dev/afdb50.tar.gz" "${TMP_PATH}/afdb50.tar.gz" downloadFile "https://foldseek.steineggerlab.workers.dev/afdb50clusearch.tar.gz" "${TMP_PATH}/afdb50clusearch.tar.gz" downloadFile "https://foldseek.steineggerlab.workers.dev/afdb50.version" "${TMP_PATH}/version" fi tar xvfz "${TMP_PATH}/afdb50.tar.gz" -C "${TMP_PATH}" tar xvfz "${TMP_PATH}/afdb50clusearch.tar.gz" -C "${TMP_PATH}" push_back "${TMP_PATH}/afdb50" INPUT_TYPE="FOLDSEEK_DB" ;; "Alphafold/Proteome") if notExists "${TMP_PATH}/alphafolddb.tar.gz"; then downloadFile "https://foldseek.steineggerlab.workers.dev/afdb_proteome.tar.gz" "${TMP_PATH}/afdb_proteome.tar.gz" downloadFile "https://foldseek.steineggerlab.workers.dev/afdb_proteome.version" "${TMP_PATH}/version" fi tar xvfz "${TMP_PATH}/afdb_proteome.tar.gz" -C "${TMP_PATH}" push_back "${TMP_PATH}/afdb_proteome" INPUT_TYPE="FOLDSEEK_DB" ;; "Alphafold/Swiss-Prot") if notExists "${TMP_PATH}/alphafold_swissprot.tar.gz"; then downloadFile "https://foldseek.steineggerlab.workers.dev/afdb_swissprot.tar.gz" "${TMP_PATH}/afdb_swissprot.tar.gz" downloadFile "https://foldseek.steineggerlab.workers.dev/afdb_swissprot.version" "${TMP_PATH}/version" fi tar xvfz "${TMP_PATH}/afdb_swissprot.tar.gz" -C "${TMP_PATH}" push_back "${TMP_PATH}/afdb_swissprot" INPUT_TYPE="FOLDSEEK_DB" ;; "ESMAtlas30") downloadFileList "https://raw.githubusercontent.com/facebookresearch/esm/main/scripts/atlas/v0/highquality_clust30/foldseekdb.txt" "${TMP_PATH}/" printf "v0 %s\n" "$(date "+%s")" > "${TMP_PATH}/version" push_back "${TMP_PATH}/highquality_clust30" INPUT_TYPE="FOLDSEEK_DB" ;; "PDB") if notExists "${TMP_PATH}/pdb.tar.gz"; then downloadFile "https://foldseek.steineggerlab.workers.dev/pdb100.tar.gz" "${TMP_PATH}/pdb.tar.gz" downloadFile "https://foldseek.steineggerlab.workers.dev/pdb100.version" "${TMP_PATH}/version" fi tar xvfz "${TMP_PATH}/pdb.tar.gz" -C "${TMP_PATH}" push_back "${TMP_PATH}/pdb" INPUT_TYPE="FOLDSEEK_DB" ;; esac

if notExists "${OUTDB}.dbtype"; then case "${INPUT_TYPE}" in "FOLDSEEK_DB") eval "set -- $ARR" IN="${*}" for SUFFIX in ".source" "_mapping" "_taxonomy"; do if [ -e "${IN}_seq${SUFFIX}" ]; then mv -f -- "${IN}_seq${SUFFIX}" "${OUTDB}_seq${SUFFIX}" fi if [ -e "${IN}${SUFFIX}" ]; then mv -f -- "${IN}${SUFFIX}" "${OUTDB}${SUFFIX}" fi done

    for SUFFIX in "" "_ss" "_h" "_ca"; do
        if [ -e "${IN}_seq${SUFFIX}.dbtype" ]; then
            # shellcheck disable=SC2086
            "${MMSEQS}" mvdb "${IN}_seq${SUFFIX}" "${OUTDB}_seq${SUFFIX}" || fail "mv died"
        fi
        # shellcheck disable=SC2086
        "${MMSEQS}" mvdb "${IN}${SUFFIX}" "${OUTDB}${SUFFIX}" || fail "mv died"
    done

    if [ -e "${IN}_clu.dbtype" ]; then
        # shellcheck disable=SC2086
        "${MMSEQS}" mvdb "${IN}_clu" "${OUTDB}_clu" || fail "mv died"
    fi
;;

esac fi

if [ -n "${TAXONOMY}" ] && notExists "${OUTDB}_mapping"; then case "${INPUT_TYPE}" in "FOLDSEEK_DB") eval "set -- $ARR" IN="${*}" mv -f -- "${IN}_mapping" "${OUTDB}_mapping" mv -f -- "${IN}_taxonomy" "${OUTDB}_taxonomy" if [ -e "${IN}_seq.dbtype" ]; then mv -f -- "${IN}_seq_mapping" "${OUTDB}_seq_mapping" mv -f -- "${IN}_seq_taxonomy" "${OUTDB}_seq_taxonomy" fi ;; esac fi

if notExists "${OUTDB}.version"; then mv -f "${TMP_PATH}/version" "${OUTDB}.version" fi

if [ -n "${REMOVE_TMP}" ]; then rm -f "${TMP_PATH}/download.sh" fi `

steineggerlab / foldseek

There seem to be some minor issues with downloading pre-generated databases using databases. #253

shellcheck disable=SC1003

check number of input variables