Stampede2 TACC/Unix Exercise

Get your data

#IF YOU HAVE NOT COPIED OVER DATA ALREADY, DO THE FOLLOWING:
cds
mkdir my_rnaseq_course #this is where you'll be doing all the course exercises
cd my_rnaseq_course
cp -r /work2/projects/BioITeam/projects/courses/rnaseq_course/day_1_partA .  #for this specific exercise

cds
cd my_rnaseq_course/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 stampede2 account (under day_1_partA/tacc_exercise)

    Hint

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

    Answer

   #Open terminal
   #Go to where genes.1 got downloaded (most likely Downloads)
   cd ~/Downloads
   scp genes.1 <username>@stampede2.tacc.utexas.edu:/scratch/*/<username>/my_rnaseq_course/day_1_partA/tacc_exercise

2. 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.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=RNASeq-Mon

    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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