changeset 8:29eeddd8ea62 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 1429f00733ee24bf2edf56b9fd7ff4ad2dec3f15

--- a/launch_gnb.sh	Thu Feb 01 12:45:00 2024 +0000
+++ b/launch_gnb.sh	Tue Feb 20 10:05:05 2024 +0000
@@ -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"
@@ -26,8 +29,15 @@
 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))"
 
+# 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=$!
@@ -38,7 +48,8 @@
 
   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 +58,9 @@
 
   sleep 3
 done;
+
+# Make sure that gnb is working, and that it's serving on the expected port
+curl "http://127.0.0.1:${GNB_PORT}/healthcheck" > /dev/null
+grep -q "Healthcheck OK" ./gnb.log
+
+echo "GNB is ready"

--- a/macros.xml	Thu Feb 01 12:45:00 2024 +0000
+++ b/macros.xml	Tue Feb 20 10:05:05 2024 +0000
@@ -7,7 +7,7 @@
         </requirements>
     </xml>
 
-    <token name="@TOOL_VERSION@">0.4.12</token>
+    <token name="@TOOL_VERSION@">0.4.13</token>
     <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy0</token>
 
     <xml name="citation">
@@ -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;