Use tmp on databases dir for setup_db.sh

soedinglab · Jul 30, 2024 · 2e8b603 · 2e8b603
1 parent 525531e
commit 2e8b603
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/docker-compose/docker-compose.yml b/docker-compose/docker-compose.yml
@@ -49,9 +49,7 @@ services:
     entrypoint: /usr/local/bin/setup_db.sh
     volumes:
       - ./setup_db.sh:/usr/local/bin/setup_db.sh:ro
-      - ${DB_PATH}:/opt/mmseqs-web/databases
-    tmpfs:
-      - /tmp:exec
+      - ${DB_PATH}:/opt/mmseqs-web/databases:rw
     profiles:
       - setup
     environment:

diff --git a/docker-compose/setup_db.sh b/docker-compose/setup_db.sh
@@ -8,13 +8,15 @@ for DB in "${@}"; do
 
 SAFE=$(echo "${DB}" | tr -cd '[a-zA-Z0-9]._-')
 if [ ! -e "/opt/mmseqs-web/databases/${SAFE}.dbtype" ]; then
-    "${APP}" databases "${DB}" "/opt/mmseqs-web/databases/${SAFE}" /tmp || continue
+    "${APP}" databases "${DB}" "/opt/mmseqs-web/databases/${SAFE}" "/opt/mmseqs-web/databases/tmp_${SAFE}" || continue
 fi
 
 if [ ! -e "/opt/mmseqs-web/databases/${SAFE}.idx.dbtype" ]; then
-    "${APP}" createindex "/opt/mmseqs-web/databases/${SAFE}" /tmp --split 1
+    "${APP}" createindex "/opt/mmseqs-web/databases/${SAFE}" "/opt/mmseqs-web/databases/tmp_${SAFE}" --split 1
 fi
 
+rm -rf -- "/opt/mmseqs-web/databases/tmp_${SAFE}"
+
 VERSION=$(cat "/opt/mmseqs-web/databases/${SAFE}.version" | head -n1 | awk '{ print $1; }')
 TAXONOMY=$("${APP}" databases --tsv | awk -v db="${DB}" '$1 == db { printf("%s", $3); f=1; exit; } END { if (f==0) printf("false"); }')