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Stampede2 TACC/Unix Exercise
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 -> genes.1 and transfer it to your stampede2 account (under day_1_partA/tacc_exercise)
Make a commands file with the unix commands.
Use launcher_creator.py to create a launcher to submit this job (command file).
Submit the job.
Use our summer school reservation when submitting jobs to get higher priority:
sbatch --reservation=RNASeq-Mon
Check the queue.
Check the output files and log files.
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