Mercurial > repos > gga > genenotebook_genenotebook_build
comparison launch_gnb.sh @ 1:f415e44e71de draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
author | gga |
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date | Mon, 03 Apr 2023 15:01:52 +0000 |
parents | 22f22c3e81bf |
children | 5a6050937cb9 |
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0:22f22c3e81bf | 1:f415e44e71de |
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2 | 2 |
3 set -e | 3 set -e |
4 | 4 |
5 mongod --dbpath ./mongo_db/ --unixSocketPrefix `pwd` --bind_ip fake_socket --logpath ./mongod.log --pidfilepath ./mongo.pid & | 5 mongod --dbpath ./mongo_db/ --unixSocketPrefix `pwd` --bind_ip fake_socket --logpath ./mongod.log --pidfilepath ./mongo.pid & |
6 | 6 |
7 sleep 5 | 7 sleep 8 |
8 | 8 |
9 # "waiting for connections on port" is for mongodb 4x | |
10 #if ! grep -q "waiting for connections on port" ./mongod.log; then | |
11 # "Listening on" is for mongodb 5x | 9 # "Listening on" is for mongodb 5x |
12 if ! grep -q "Listening on" ./mongod.log; then | 10 if ! grep -q "Listening on" ./mongod.log; then |
13 echo "Failed to launch MongoDB:" 1>&2; | 11 echo "Failed to launch MongoDB:" 1>&2; |
14 cat ./mongod.log 1>&2; | 12 cat ./mongod.log 1>&2; |
15 kill $GNB_PID; | 13 kill $GNB_PID; |
17 fi; | 15 fi; |
18 | 16 |
19 TMP_STORAGE=$(pwd)/tmp_storage | 17 TMP_STORAGE=$(pwd)/tmp_storage |
20 mkdir "$TMP_STORAGE" | 18 mkdir "$TMP_STORAGE" |
21 | 19 |
22 genenotebook run --storage-path "$TMP_STORAGE" --port ${GNB_PORT} --mongo-url mongodb://$MONGO_URI%2Fmongodb-27017.sock/genenotebook > ./gnb.log 2>&1 & | 20 genoboo run --storage-path "$TMP_STORAGE" --port ${GNB_PORT} --mongo-url mongodb://$MONGO_URI%2Fmongodb-27017.sock/genenotebook > ./gnb.log 2>&1 & |
23 | 21 |
24 export GNB_PID=$! | 22 export GNB_PID=$! |
25 | 23 |
26 sleep 15 | 24 sleep 15 |
27 | 25 |