How to write Unix shell scripts with options? - Stack Overflow.
I call this the unofficial bash strict mode. This causes bash to behave in a way that makes many classes of subtle bugs impossible. You'll spend much less time debugging, and also avoid having unexpected complications in production. There is a short-term downside: these settings make certain common bash idioms harder to work with.
Bash Shell has several special positional parameters which can be referenced but can not be assigned. These bash parameters are used to process command line arguments in a bash shell script, to get process status, exit status and options flag.
Answer to What you should do: 1- Write a bash script that checks if options a, b, c, and d where used by the user when your script.
Question: Write A Bash Script That Checks If Options A, B And C Where Invoked By The User When Your Script Was Called. You May Consider Using GETOPTS And CASE Statements Command To Handle Options Passed To Your Script. In Your Script: (i) Only Option A Expects Its Own Argument (ii) Display To The Screen (terminal) Information Which, If Any, Option Was Triggered.
Now let's see some example bash scripts and qsub commands that submit those jobs to the cluster. Submitting a bowtie job. Bowtie is a short-read aligner used to align reads from next-gen sequencing machines. The script includes the commandline options within it, so no need to pass those options on the commandline.