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echo "My name is _____ and todays date is:" > GVA2021.output.txt date >> GVA2021.output.txt echo "I have just demonstrated that I know how to redirect output to a new file, and to append things to an already created file. Or at least thats what I think I did" >> GVA2021.output.txt echo "i'm going to test this by counting the number of lines in the file that I am writing to. So if the next line reads 4 I remember I'm on the right track" >> GVA2021.output.txt wc -l GVA2021.output.txt >> GVA2021.output.txt echo "I know that normally i would be typing commands on each line of this file, that would be executed on a compute node instead of the head node so that my programs run faster, in parallel, and do not slow down others or risk my tacc account being locked out" >> GVA2021.output.txt echo "i'm currently in my scratch directory on stampede2. there are 2 main ways of getting here: cds and cd $SCRATCH" >>GVA2021.output.txt pwd >> GVA2021.output.txt echo "over the last week I've conducted multiple different types of analysis on a variety of sample types and under different conditions. Each of the exercises was taken from the website https://wikis.utexas.edu/display/bioiteam/Genome+Variant+Analysis+Course+2021" >> GVA2021.output.txt echo "using the ls command i'm now going to try to remind you (my future self) of what tutorials I did" >> GVA2021.output.txt ls -1 >> GVA2021.output.txt echo "the contents of those directories (representing the data i downloaded and the work i did) are as follows: ">> GVA2021.output.txt find . >> GVA2021.output.txt echo "the commands that i have run on the headnode are: " >> GVA2021.output.txt history >> GVA2021.output.txt echo "the contents of this, my commands file are: ">>GVA2021.output.txt cat commands >> GVA2021.output.txt echo "thisI will createnext creat a what_i_did_at_GVA2021.slurm file that will run for 15 minutes" >> GVA2021.output.txt echo "and i will send this job to the queue using the the command: sbatch what_i_did_at_GVA2021.slurm" >> GVA2021.output.txt |
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cp /corral-repl/utexas/BioITeam/gva_course/GVA2021.launcher.slurm launcherwhat_i_did_at_GVA2021.slurm nano launcherwhat_i_did_at_GVA2021.slurm |
As stated above things we want to change are:
| Line number | As is | To be |
|---|---|---|
| 16 | #SBATCH -J jobName | #SBATCH -J end_of_class |
| 21 | #SBATCH -t 12:00:00 | #SBATCH -t 0:10:00 |
| 27 | conda activate GVA2021 | conda activate GVA2021 |
Line 27 could be detled deleted if you prefer.
Again use ctl-o and ctl-x to save the file and exit.
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sbatch launcherwhat_i_did_at_GVA2021.slurm |
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wc -l commands |
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