Get your data
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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 -> 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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