check port at the last moment

galaxy-genome-annotation · Feb 2, 2024 · 76ae329 · 76ae329
1 parent 6f1ddc5
commit 76ae329
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/tools/genenotebook/launch_gnb.sh b/tools/genenotebook/launch_gnb.sh
@@ -26,8 +26,6 @@ while ! grep -q "Listening on" ./mongod.log; do
   sleep 3
 done;
 
-echo "Mongod is ready, starting gnb now on port ${GNB_PORT} and with mongodb://${MONGO_URI}%2Fmongodb-27017.sock/genenotebook"
-
 TMP_STORAGE=$(pwd)/tmp_storage
 mkdir "$TMP_STORAGE"
 
@@ -36,6 +34,10 @@ touch gnb.log
 
 export NODE_OPTIONS="--max-old-space-size=$((${GALAXY_MEMORY_MB:-8192} * 75 / 100))"
 
+# Find free port at the last moment
+export GNB_PORT=$(bash "$(dirname "${BASH_SOURCE[0]}")/find_free_port.sh")
+echo "Mongod is ready, starting gnb now on port ${GNB_PORT} and with mongodb://${MONGO_URI}%2Fmongodb-27017.sock/genenotebook"
+
 genoboo run --storage-path "$TMP_STORAGE" --port ${GNB_PORT} --mongo-url mongodb://$MONGO_URI%2Fmongodb-27017.sock/genenotebook > ./gnb.log 2>&1 &
 
 export GNB_PID=$!

diff --git a/tools/genenotebook/macros.xml b/tools/genenotebook/macros.xml
@@ -37,7 +37,6 @@
     For some unknwon reason, unixSocketPrefix needs an absolute path
     -->
     <token name="@START_GNB@"><![CDATA[
-        export GNB_PORT="\$(bash '$__tool_directory__/find_free_port.sh')";
         export MONGO_URI="\$(pwd | sed 's|/|%2F|g')";
         #if $existing
             tar -xf '${existing}' mongo_db;