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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)
Expand title Hint Use the scp command from your computer (or winscp if its a windows machine)
Expand title Answer Code Block #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.
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)
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
Submit the job.
Warning Use our summer school reservation when submitting jobs to get higher priority:
sbatch --reservation=RNAday1RNASeq-Mon
Expand title Hint sbatch
Expand title Answer Code Block sbatch exercise.slurm
Check the queue.
Expand title Answer Code Block showq -u <username>
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
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