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Commit message:
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 1429f00733ee24bf2edf56b9fd7ff4ad2dec3f15 |
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modified:
launch_gnb.sh macros.xml |
| b |
| 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" |
| b |
| 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 @@ </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; |