Mercurial > repos > gga > genenotebook_genenotebook_build
changeset 7:dfb2bc3aedbd draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 91ccbf9f293fe6b183302841aa49e061c4ab3157
| author | gga |
|---|---|
| date | Thu, 01 Feb 2024 12:45:00 +0000 |
| parents | 12494257f0f0 |
| children | 29eeddd8ea62 |
| files | launch_gnb.sh macros.xml test-data/output/genome.tar.bz2 test-data/output/genome_annot.tar.bz2 test-data/output/genome_annot_ips.tar.bz2 test-data/output/genome_annot_ips_en.tar.bz2 test-data/output/genome_annot_ips_en_bl_exp.tar.bz2 test-data/output/genome_reload.tar.bz2 |
| diffstat | 8 files changed, 32 insertions(+), 16 deletions(-) [+] |
line wrap: on
line diff
--- a/launch_gnb.sh Fri Nov 17 15:53:01 2023 +0000 +++ b/launch_gnb.sh Thu Feb 01 12:45:00 2024 +0000 @@ -2,17 +2,26 @@ set -e -mongod --dbpath ./mongo_db/ --unixSocketPrefix `pwd` --bind_ip fake_socket --logpath ./mongod.log --pidfilepath ./mongo.pid & +echo "Running mongod: " +mongod --dbpath ./mongo_db/ --unixSocketPrefix "$(pwd)" --bind_ip fake_socket --logpath ./mongod.log --pidfilepath ./mongo.pid & -sleep 8 +echo "Waiting while mongod starts up" + +tries=0 # "Listening on" is for mongodb 5x -if ! grep -q "Listening on" ./mongod.log; then - echo "Failed to launch MongoDB:" 1>&2; - cat ./mongod.log 1>&2; - kill $GNB_PID; - exit 1; -fi; +while ! grep -q "Listening on" ./mongod.log; do + + tries=$((tries + 1)) + + if [ "$tries" -ge 30 ]; then + echo "Failed to launch MongoDB:" 1>&2; + cat ./mongod.log 1>&2; + exit 1; + fi + + sleep 3 +done; TMP_STORAGE=$(pwd)/tmp_storage mkdir "$TMP_STORAGE" @@ -23,11 +32,18 @@ export GNB_PID=$! -sleep 15 +tries_gnb=0 + +while ! grep -q "GeneNoteBook server started, serving" ./gnb.log; do + + tries_gnb=$((tries_gnb + 1)) -if ! grep -q "GeneNoteBook server started, serving" ./gnb.log; then - echo "Failed to launch GeneNoteBook:" 1>&2; - cat ./gnb.log 1>&2; - kill $GNB_PID $(<"./mongo.pid"); - exit 1; -fi; + if [ "$tries_gnb" -ge 30 ]; then + echo "Failed to launch GeneNoteBook:" 1>&2; + cat ./gnb.log 1>&2; + kill $GNB_PID $(<"./mongo.pid"); + exit 1; + fi + + sleep 3 +done;
--- a/macros.xml Fri Nov 17 15:53:01 2023 +0000 +++ b/macros.xml Thu Feb 01 12:45:00 2024 +0000 @@ -7,7 +7,7 @@ </requirements> </xml> - <token name="@TOOL_VERSION@">0.4.9</token> + <token name="@TOOL_VERSION@">0.4.12</token> <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy0</token> <xml name="citation">