Mercurial > repos > gga > genenotebook_genenotebook_build

comparison launch_gnb.sh @ 13:eae124b1e1f1 draft default tip

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 27cd61679954c8a70075dbc190e3f246b0b6c7f4
author gga
date Tue, 15 Jul 2025 13:09:49 +0000
parents 4398a6fea625
children
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12:23effb1dfe1a 13:eae124b1e1f1
10 10
11 echo "Waiting while mongod starts up" 11 echo "Waiting while mongod starts up"
12 12
13 tries=0 13 tries=0
14 14
15 # "Listening on" is for mongodb 5x 15 # "Listening on" is for mongodb 150x
16 while ! grep -q "Listening on" ./mongod.log; do 16 while ! grep -q "Listening on" ./mongod.log; do
17 17
18 tries=$((tries + 1)) 18 tries=$((tries + 1))
19 19
20 if [ "$tries" -ge 50 ]; then 20 if [ "$tries" -ge 150 ]; then
21 echo "Failed to launch MongoDB:" 1>&2; 21 echo "Failed to launch MongoDB:" 1>&2;
22 cat ./mongod.log 1>&2; 22 cat ./mongod.log 1>&2;
23 exit 1; 23 exit 1;
24 fi 24 fi
25 25
47 while ! grep -q "GeneNoteBook server started, serving" ./gnb.log; do 47 while ! grep -q "GeneNoteBook server started, serving" ./gnb.log; do
48 48
49 tries_gnb=$((tries_gnb + 1)) 49 tries_gnb=$((tries_gnb + 1))
50 50
51 # GNB can take a while to start depending on storage (accessing many many small js files) 51 # GNB can take a while to start depending on storage (accessing many many small js files)
52 if [ "$tries_gnb" -ge 150 ]; then 52 if [ "$tries_gnb" -ge 250 ]; then
53 echo "Failed to launch GeneNoteBook:" 1>&2; 53 echo "Failed to launch GeneNoteBook:" 1>&2;
54 cat ./gnb.log 1>&2; 54 cat ./gnb.log 1>&2;
55 kill $GNB_PID $(<"./mongo.pid"); 55 kill $GNB_PID $(<"./mongo.pid");
56 exit 1; 56 exit 1;
57 fi 57 fi
64 64
65 tries_curl=0 65 tries_curl=0
66 66
67 while ! curl -s "http://127.0.0.1:${GNB_PORT}/healthcheck"; do 67 while ! curl -s "http://127.0.0.1:${GNB_PORT}/healthcheck"; do
68 tries_curl=$((tries_curl + 1)) 68 tries_curl=$((tries_curl + 1))
69 if [ "$tries_curl" -ge 100 ]; then 69 if [ "$tries_curl" -ge 200 ]; then
70 echo "Healthcheck is not working, stopping:" 1>&2; 70 echo "Healthcheck is not working, stopping:" 1>&2;
71 cat ./gnb.log 1>&2; 71 cat ./gnb.log 1>&2;
72 kill $GNB_PID $(<"./mongo.pid"); 72 kill $GNB_PID $(<"./mongo.pid");
73 exit 1; 73 exit 1;
74 fi 74 fi
76 sleep 3 76 sleep 3
77 done; 77 done;
78 78
79 grep -q "Healthcheck OK" ./gnb.log 79 grep -q "Healthcheck OK" ./gnb.log
80 80
81 sleep 30
82
81 echo "GNB is ready" 83 echo "GNB is ready"