Page Comparison

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

...

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)

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

   Expand
   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.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.
   
   

   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.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).

   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 UT-2015-05-18

4. Submit the job.

   Warning
   Use our summer school reservation when submitting jobs to get higher priority: sbatch --reservation=CCBBintro_Day_1NGS

   Expand
   title Hint
   sbatch

   Expand
   title Answer
   Code Block sbatch exercise.slurm

   
   

   
   

5. Check the queue.

   Expand
   title Answer
   Code Block showq -u <username>

6. 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

...