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Full Discussion: Bash code change
Top Forums Shell Programming and Scripting Bash code change Post 302945325 by cmccabe on Thursday 28th of May 2015 10:28:50 AM
Old 05-28-2015
Bash code change

I have the below bash which runs great. Before I make a change I wanted to check with experts (as I am not one). After the perl code completes, I am going to display "annotation complete" then go into the remove function .

Code:
 
annovar() {
    # combine id and position files
	cd 'C:\Users\cmccabe\Desktop\annovar'
	cp out_parse.txt "$(cat target.txt)"
	
	# run annotation
              $( perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f ")' < target.txt )
			  
     printf "The annotation is complete, would you like analyze additional target gene patients? Y/N "; read match_choice
	 case "$match_choice" in
        [yY]) id="${id}"; menu ;;
        [nN]) id="${id}"; remove ;;
		esac
}

My question is will something like this work: Thank you Smilie.

Code:
annovar() {
    # combine id and position files
	cd 'C:\Users\cmccabe\Desktop\annovar'
	cp out_parse.txt "$(cat target.txt)"
	
	# run annotation
              $( perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f ")' < target.txt )
			  
     printf "The annotation is complete "; remove
	  esac
}

 

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SYSPROFILE(8)						      System Manager's Manual						     SYSPROFILE(8)

NAME
sysprofile - modular centralized shell configuration DESCRIPTION
sysprofile is a generic approach to configure shell settings in a modular and centralized way mostly aimed at avoiding work for lazy sysad- mins. It has only been tested to work with the bash shell. It basically consists of the small /etc/sysprofile shell script which invokes other small shell scripts having a .bash suffix which are contained in the /etc/sysprofile.d/ directory. The system administrator can drop in any script he wants without any naming convention other than that the scripts need to have a .bash suffix to enable automagic sourcing by /etc/sysprofile. This mechanism is set up by inserting a small shell routine into /etc/profile for login shells and optionally into /etc/bashrc and/or /etc/bash.bashrc for non-login shells from where the actual /etc/sysprofile script is invoked: if [ -f /etc/sysprofile ]; then . /etc/sysprofile fi For using "sysprofile" under X11, one can source it in a similar way from /etc/X11/Xsession or your X display manager's Xsession file to provide the same shell environment as under the console in X11. See the example files in /usr/share/doc/sysprofile/ for illustration. For usage of terminal emulators with a non-login bash shell under X11, take care to enable sysprofile via /etc/bash.bashrc. If not set this way, your terminal emulators won't come up with the environment defined by the scripts in /etc/sysprofile.d/. Users not wanting /etc/sysprofile to be sourced for their environment can easily disable it's automatic mechanism. It can be disabled by simply creating an empty file called $HOME/.nosysprofile in the user's home directory using e.g. the touch(1) command. Any single configuration file in /etc/sysprofile.d/ can be overridden by any user by creating a private $HOME/.sysprofile.d/ directory which may contain a user's own version of any configuration file to be sourced instead of the system default. It's names have just to match exactly the system's default /etc/sysprofile.d/ configuration files. Empty versions of these files contained in the $HOME/.syspro- file.d/ directory automatically disable sourcing of the system wide version. Naturally, users can add and include their own private script inventions to be automagically executed by /etc/sysprofile at login time. OPTIONS
There are no options other than those dictated by shell conventions. Anything is defined within the configuration scripts themselves. SEE ALSO
The README files and configuration examples contained in /etc/sysprofile.d/ and the manual pages bash(1), xdm(1x), xdm.options(5), and wdm(1x). Recommended further reading is everything related with shell programming. If you need a similar mechanism for executing code at logout time check out the related package syslogout(8) which is a very close compan- ion to sysprofile. BUGS
sysprofile in its current form is mainly restricted to bash(1) syntax. In fact it is actually a rather embarrassing quick and dirty hack than anything else - but it works. It serves the practical need to enable a centralized bash configuration until something better becomes available. Your constructive criticism in making this into something better" is very welcome. Before i forget to mention it: we take patches... ;-) AUTHOR
sysprofile was developed by Paul Seelig <pseelig@debian.org> specifically for the Debian GNU/Linux system. Feel free to port it to and use it anywhere else under the conditions of either the GNU public license or the BSD license or both. Better yet, please help to make it into something more worthwhile than it currently is. SYSPROFILE(8)
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