Lonestar5 TACC/Unix Exercise

Get your data

cds
cd my_rnaseq_course
cd day_1_partA/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.  First you need all the files. One is missing. Download it from here -> genes.1  and transfer it to your lonestar5 account (under day_1_partA/tacc_exercise)

    Hint

   Use the scp command from your computer (or winscp if its a windows machine)

    Answer

   #FOR MAC: 
   #Open terminal
   #Go to where genes.1 got downloaded (most likely Downloads)
   cd ~/Downloads
   scp genes.1 <username>@ls5.tacc.utexas.edu:/scratch/*/<username>/my_rnaseq_course/day_1_partA/tacc_exercise
   
   
   #FOR WINDOWS:
   Use winscp (free to download) to drag and drop the files from your computer to the server (in the right directory).

2. Make a commands file with the unix commands to print the first 10 lines of each file into an output file.
   
   

    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.1
   head genes.2 > head.2
   head genes.3 > head.3
   head genes.4 > head.4 
    
   #ctrl+x to exit (then Y to save)

3. 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 UT-2015-05-18

4. Submit the job.

   Use our summer school reservation when submitting jobs to get higher priority:

   sbatch --reservation=intro_NGS
   

    Hint

   sbatch

    Answer

   sbatch exercise.slurm

   
   

   
   

5. Check the queue.

    Answer

   showq -u <username>

6. 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

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