# HG changeset patch
# User gga
# Date 1706791500 0
# Node ID dfb2bc3aedbd0a8610b67a77dcdcce4f2f197d91
# Parent  12494257f0f0ce87211b5ae1c4b9987e797ff508
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 91ccbf9f293fe6b183302841aa49e061c4ab3157

diff -r 12494257f0f0 -r dfb2bc3aedbd launch_gnb.sh
--- 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;
diff -r 12494257f0f0 -r dfb2bc3aedbd macros.xml
--- 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">
diff -r 12494257f0f0 -r dfb2bc3aedbd test-data/output/genome.tar.bz2
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diff -r 12494257f0f0 -r dfb2bc3aedbd test-data/output/genome_annot.tar.bz2
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diff -r 12494257f0f0 -r dfb2bc3aedbd test-data/output/genome_annot_ips.tar.bz2
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diff -r 12494257f0f0 -r dfb2bc3aedbd test-data/output/genome_annot_ips_en.tar.bz2
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diff -r 12494257f0f0 -r dfb2bc3aedbd test-data/output/genome_annot_ips_en_bl_exp.tar.bz2
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diff -r 12494257f0f0 -r dfb2bc3aedbd test-data/output/genome_reload.tar.bz2
Binary file test-data/output/genome_reload.tar.bz2 has changed