TACC/Unix Exercise

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.
   
   

    Hint

   Open an editor to create a file called commands

   Use head command to print the first 10 lines.

    Answer

   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).

    Hint

   launcher_creator.py -h to see the options.

    Answer

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

3. Submit the job.

    Hint

   qsub

    Answer

   qsub exercise.sge

4. Check the queue.

    Answer

   qstat

5. Check the output files and log files.

    Hint

   Look at <jobname>.o* file for output information

   Look at <jobname>.e* file for log/error information

    Answer

   less exercise.o* #q to exit
   less exercise.e* #q to exit