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cp $WORK/my_fastq_data/*fastq $SCRATCH/my_project/ |
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cat commands > commands.out # this will print the contents of the file you are currently editing to a new file called commands.out date > date.out # this will create a file with todays date on it pwd > current_directory.out # this will create a file with the current directory in it echo "my name is <YOURNAME>" >> name.out # Note that this time we used the append symbol >> not the write symbol > as we plan to put multiple things into the same file. Be sure to replace the <> signs with your name echo "This is the final result of my first script. It worked how I thought it would, or hopefully have the resources to figure out why it didn't" >> name.out # this will add another line of text to the name.out file. # feel free to add up to 7 more lines to your commands file here using the cat/ls/pwd/mkdir/other commands that you know. # beware using cd commands here as it will change your directory as if you were doing it on an interactive node and may cause you to reference files that don't exist commands that you know. # beware using cd commands here as it will change your directory as if you were doing it on an interactive node and may cause you to reference files that don't exist |
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In the next code box you see the top line is commented out but says to hit 'ctrl-o' 'ctrl-x' to write and exit nano. Since files that you open with nano are able to be edited immediately, it is a good idea to get in the habit of only saving files when you explicitly know you meant to edit them with the ctrl-o command (control + o) and then when you hit ctrl-x (control + x) nano exits gracefully. Conversely, if you open a file with nano with the intent of just looking at it or decide not to make any changes, or want to get rid of all your changes, you can hit ctrl-x and exit nano without saving the changes. If you instead choose to exit nano with ctrl-x and then select 'save' you risk building a habit of always saving when you exit and thus may introduce edits to your files you didn't mean to. |
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# write and exit nano now ctrl-o ctrl-x launcher_creator.py -n "my_first_job" -j commands -t 00:02:00 -a "UT-2015-05-18" # this will create a my_first_job.slurm file that will run for 2 minutes sbatch my_first_job.slurm # this will actually submit the job to the Queue Manager and if everything has gone right, it will be added to the development queue. |
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As this tutorial is focused only on downloading interesting programs you may read about, this is the final step. If you do the optional trimmomatic tutorial later in the course, we'll go over some of the nuances of trimmomatic and shortcuts to make it easier to use. This page will be updated to include a link to said tutorial later in the week.
wget alternative
It is always an alternative to download such files directly to your computer using a web browser and then use the scp command to transfer it to TACC. The wget command can help you avoid these intermediate steps and is more convenient most of the time unless you want to install the program on both your laptop and TACC, and have the same operating system on both.
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If you still see something else, let the instructor know.
The multiqc tutorial can be found here.
This concludes the the linux and lonestar refresher/introduction tutorial.
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