# HG changeset patch # User gga # Date 1708423505 0 # Node ID 29eeddd8ea6252fa718bdf7484b09c96ed0bab8d # Parent dfb2bc3aedbd0a8610b67a77dcdcce4f2f197d91 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 1429f00733ee24bf2edf56b9fd7ff4ad2dec3f15 diff -r dfb2bc3aedbd -r 29eeddd8ea62 launch_gnb.sh --- 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" diff -r dfb2bc3aedbd -r 29eeddd8ea62 macros.xml --- 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 @@ - 0.4.12 + 0.4.13 @TOOL_VERSION@+galaxy0 @@ -37,7 +37,6 @@ For some unknwon reason, unixSocketPrefix needs an absolute path -->