Add new file - canto_running_log.sh

This script prints all the activity log from the running canto-server container into the file 'canto_running.log' in the 'logs' sub-folder of 'canto-space'

canto_running_log.sh

+#!/bin/bash
+
+#this script prints all the activity log messages from the running canto-server container into the file 'canto_running.log' in the 'logs' sub-folder of 'canto-space'
+
+# Define canto-space root
+CANTOSPACE="/data/export/canto-space"
+
+# Define logs folder inside canto-space
+LOGS="logs"
+
+# Define log file
+LOGFILE="${CANTOSPACE}/${LOGS}/canto_server_running.log"
+
+#this line retrieves the canto container id
+DOCKERNAME=$(docker ps -a --filter status=running | awk '$2 ~ /pombase\/canto-run/ { print $1 }')
+
+	if [[ ! -z "${DOCKERNAME}" ]]; then
+	echo "Canto running on container ${DOCKERNAME} - see canto_server_running.log for the log messages"
+	
+	# Redirect all output to logfile
+	exec &> "${LOGFILE}"
+	
+	#docker logs is docker's command to retrieve all log messages from a specific container
+	docker logs "${DOCKERNAME}"
+
+	else echo "Canto not running - no log messages to show"
+	
+  fi
+
+exit
\ No newline at end of file