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Comment: Migrated to Confluence 5.3

Get your data

Code Block
titleGet set up
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
    titleHint

    Open an editor to create a file called commands

    Use head command to print the first 10 lines.

    Expand
    titleAnswer
    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
    titleHint

    launcher_creator.py -h to see the options.

    Expand
    titleAnswer
    Code Block
    launcher_creator.py -n exercise -t 01:00:00 -j commands -q development -a CCBB
  3. Submit the job.

    Expand
    titleHint

    qsub

    Expand
    titleAnswer
    Code Block
    qsub exercise.sge
  4. Check the queue.

    Expand
    titleAnswer
    Code Block
    qstat
  5. Check the output files and log files.

    Expand
    titleHint

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

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

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

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