There are many ways you can do it.
(1) Cascading jobs
Create the JobConf object "job1" for the first job and set all the parameters with "input" as inputdirectory and "temp" as output directory. Execute this job: JobClient.run(job1).
Immediately below it, create the JobConf object "job2" for the second job and set all the parameters with "temp" as inputdirectory and "output" as output directory. Execute this job: JobClient.run(job2).
(2) Create two JobConf objects and set all the parameters in them just like (1) except that you don't use JobClient.run.
Then create two Job objects with jobconfs as parameters:
Job job1=new Job(jobconf1); Job job2=new Job(jobconf2);
Using the jobControl object, you specify the job dependencies and then run the jobs:
JobControl jbcntrl=new JobControl("jbcntrl");
jbcntrl.addJob(job1);
jbcntrl.addJob(job2);
job2.addDependingJob(job1);
jbcntrl.run();
(3) If you need a structure somewhat like Map+ | Reduce | Map*, you can use the ChainMapper and ChainReducer classes that come with Hadoop version 0.19 and onwards. Note that in this case, u can use only one reducer but any number of mappers before or after it.
Cheers