Can I configure an alert to run a custom script and then send an email with the output?
"run a script" action is deprecated i.e. alerts that triggered scripts to run .Custom alert actions have replaced them and can do the same and more, with a better user experience.If you have a scripted alert that you want to convert, try following these docs to create an alert action using the script you already have. http://docs.splunk.com/Documentation/Splunk/latest/AdvancedDev/ModAlertsIntro also refer https://answers.splunk.com/answers/474448/how-to-run-a-script-as-an-alert-action.html
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