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| Code Block | ||||
|---|---|---|---|---|
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mkdir fastqc_output cp /corral-repl/utexas/BioITeam/gva_course/GVA2022GVA.launcher.slurm fastqc.slurm nano multiqcfastqc.slurm |
Again while in nano you will edit most of the same lines you edited in the in the breseq tutorial. Note that most of these lines have additional text to the right of the line. This commented text is present to help remind you what goes on each line, leaving it alone will not hurt anything, removing it may make it more difficult for you to remember what the purpose of the line is
| Line number | As is | To be |
|---|---|---|
| 16 | #SBATCH -J jobName | #SBATCH -J multiqc |
| 17 | #SBATCH -n 1 | #SBATCH -n 48 |
| 21 | #SBATCH -t 12:00:00 | #SBATCH -t 0:20:00 |
| 22 | ##SBATCH --mail-user=ADD | #SBATCH --mail-user=<YourEmailAddress> |
| 23 | ##SBATCH --mail-type=all | #SBATCH --mail-type=all |
| 29 | export LAUNCHER_JOB_FILE=commands | export LAUNCHER_JOB_FILE=breseqfastqc_commands |
The changes to lines 22 and 23 are optional but will give you an idea of what types of email you could expect from TACC if you choose to use these options. Just be sure to pay attention to these 2 lines starting with a single # symbol after editing them.
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