How do you deploy to Salesforce when you have scheduled apex jobs?

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I have been using SF migration tool, but encounter a road block: we have quite a few scheduled apex job in the system.  Although the jobs may not run, the migration tool will just error out.  Do you run into issue with schedule jobs?  If so, how do you resolve them?  Thx.

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We have an apex class that we use to abort and schedule all jobs before and after deploys. We currently run this manually by calling the methods with anonymous apex (from the dev console or SoqlXplorer), but we would ideally build this in as a step in our Bamboo deployments.

public with sharing class ProcessScheduledJobs {
	public static void scheduleAll(){
		System.schedule('jobname1','0 0 2 ? * SAT', new SomeSchedulableClass());
		System.schedule('jobname2','0 1 * * * ?', new SomeOtherSchedulableClass());
	}

	public static void abortAll(){
		// CronJobDetail.JobType = '7' represents scheduled apex jobs
		for(CronTrigger ct : [SELECT Id FROM CronTrigger WHERE CronJobDetail.JobType = '7']){
			system.abortJob(ct.Id);
		}
	}
}

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