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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_2016/day_1_partA .  #for this specific exercise
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 lonestar6 account (under day_1_partA/tacc_exercise)

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

   
   

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   title Answer
   Code Block #FOR MAC:  #Open terminal #Go to where genes.1 got downloaded (most likely Downloads) cd ~/Downloads scp genes.1 <username>@ls5<username>@ls6.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.
   
   

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   title Hint
   Open an editor to create a file called commands Use head command to print the first 10 lines.

   
   

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   title Answer
   Code Block 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).

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   title Hint
   launcher_creator.py -h to see the options.

   
   

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   title Answer
   Code Block launcher_creator.py -n exercise -t 01:00:00 -j commands -q development -a UT-2015-05-18OTH21164

   
   

4. Submit the job.

   Warning
   Use our summer school reservation when submitting jobs to get higher priority: sbatch --reservation=intro_NGSRNAseq

   
   

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   title Hint
   sbatch

   
   

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   title Answer
   Code Block sbatch exercise.slurm

   
   

   
   

5. Check the queue.

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   title Answer
   Code Block showq -u <username>

   
   

6. Check the output files and log files.

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   title Hint
   Look at <jobname>.o* file for output information Look at <jobname>.e* file for log/error information

   
   

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   title Answer
   Code Block less exercise.o* #q to exit less exercise.e* #q to exit

   
   

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