Get your data
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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.
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
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.
Expand title Answer Code Block launcher_creator.py -n exercise -t 01:00:00 -j commands -q development -a CCBB
Submit the job.
Expand title Hint qsub
Expand title Answer Code Block qsub exercise.sge
Check the queue.
Expand title Answer Code Block qstat
Check the output files and log files.
Expand 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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