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Get your data

cds
mkdir my_rnaseq_course #this is where you'll be doing all the course exercises
cd my_rnaseq_course
 
cp -r /corral-repl/utexas/BioITeam/rnaseq_course/tacc_exercise .  #for this specific exercise
cd tacc_exercise

Exercise:

Run a simple command on each of these four files. We are going to just print the first 10 lines of each file.

1. Make a commands file with the unix commands.
   
   

   Expand
   title Hint
   Open an editor to create a file called commands Use head command to print the first 10 lines.

   Expand
   title Answer
   Code Block nano commands head genes.1 head genes.2 head genes.3 head genes.4 #ctrl+x to exit

2. Use launcher_creator.py to create a launcher to submit this job (command file).

   Expand
   title Hint
   launcher_creator.py -h to see the options.

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   title Answer
   Code Block launcher_creator.py -n exercise -t 01:00:00 -j commands -q development -a CCBB

3. Submit the job.

   Expand
   title Hint
   qsub

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   title Answer
   Code Block qsub exercise.sge

...

1. Check the queue.

   Expand
   title Answer
   Code Block qstat

2. Check the output files and log files.

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   title Hint
   Look at <jobname>.o* file for output information Look at <jobname>.e* file for log/error information

   Expand
   title Answer
   Code Block less exercise.o* #q to exit less exercise.e* #q to exit

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