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

[TigerWindWood]

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
`

[milot-mirdita]

Thank you for catching this issue. Would you like to fix it and submit a pull request?

[TigerWindWood]

Thank you for your reply. I'm happy to fix the code and submit a pull request.