genotebook: startup fixes

tools/genenotebook/launch_gnb.sh

@@ -2,7 +2,10 @@
 
 set -e
 
-echo "Running mongod: "
+# Make sure the file always exists even on first grep
+touch mongod.log
+
+echo "Starting mongod, listening on unix socket in $(pwd)"
 mongod --dbpath ./mongo_db/ --unixSocketPrefix "$(pwd)" --bind_ip fake_socket --logpath ./mongod.log --pidfilepath ./mongo.pid &
 
 echo "Waiting while mongod starts up"
@@ -23,9 +26,14 @@ 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"
 
+# Make sure the file always exists
+touch gnb.log
+
 export NODE_OPTIONS="--max-old-space-size=$((${GALAXY_MEMORY_MB:-8192} * 75 / 100))"
 
 genoboo run --storage-path "$TMP_STORAGE" --port ${GNB_PORT} --mongo-url mongodb://$MONGO_URI%2Fmongodb-27017.sock/genenotebook > ./gnb.log 2>&1 &
@@ -38,7 +46,8 @@ while ! grep -q "GeneNoteBook server started, serving" ./gnb.log; do
 
   tries_gnb=$((tries_gnb + 1))
 
-  if [ "$tries_gnb" -ge 30 ]; then
+  # GNB can take a while to start depending on storage (accessing many many small js files)
+  if [ "$tries_gnb" -ge 150 ]; then
     echo "Failed to launch GeneNoteBook:" 1>&2;
     cat ./gnb.log 1>&2;
     kill $GNB_PID $(<"./mongo.pid");
@@ -47,3 +56,5 @@ while ! grep -q "GeneNoteBook server started, serving" ./gnb.log; do
 
   sleep 3
 done;
+
+echo "GNB is ready"

tools/genenotebook/macros.xml

@@ -8,7 +8,7 @@
     </xml>
 
     <token name="@TOOL_VERSION@">0.4.12</token>
-    <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy0</token>
+    <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy1</token>
 
     <xml name="citation">
         <citations>