Skip to content

Update setup_databases.sh #514

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Update setup_databases.sh #514

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 7 additions & 1 deletion setup_databases.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,11 @@ fi
downloadFile() {
URL="$1"
OUTPUT="$2"
# Check if the file already exists and is greater than 0 bytes (to avoid using partially downloaded files)
if [ -s "$OUTPUT" ]; then
echo "$OUTPUT exists and is not empty. Skipping download."
return 0
fi
set +e
for i in $STRATEGY; do
case "$i" in
Expand All @@ -46,6 +51,7 @@ downloadFile() {
fail "Could not download $URL to $OUTPUT"
}


# Make MMseqs2 merge the databases to avoid spamming the folder with files
export MMSEQS_FORCE_MERGE=1

Expand Down Expand Up @@ -98,4 +104,4 @@ if [ ! -f PDB_MMCIF_READY ]; then
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
fi