Stampede2 TACC/Unix Exercise

Get your data

Get set up

#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

Move into the correct directory

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.

First you need all the files. One is missing. Download it from here -> and transfer it to your stampede2 account (under day_1_partA/tacc_exercise)
Use the scp command from your computer (or winscp if its a windows machine)
#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
Make a commands file with the unix commands.

Open an editor to create a file called commands Use head command to print the first 10 lines.
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)
Use launcher_creator.py to create a launcher to submit this job (command file).
launcher_creator.py -h to see the options.
launcher_creator.py -n exercise -t 01:00:00 -j commands -q development -a UT-2015-05-18
Submit the job.
Use our summer school reservation when submitting jobs to get higher priority:
sbatch --reservation=RNASeq-Mon
sbatch
sbatch exercise.slurm
Check the queue.
showq -u <username>
Check the output files and log files.
Look at <jobname>.o* file for output information Look at <jobname>.e* file for log/error information
less exercise.o* #q to exit less exercise.e* #q to exit

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