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Full Discussion: Batch or not if/then
Top Forums Shell Programming and Scripting Batch or not if/then Post 302922297 by Corona688 on Thursday 23rd of October 2014 03:24:13 PM
Old 10-23-2014
Quote:
Originally Posted by cmccabe
Code:
  bash ~/test.sh
/home/cmccabe/test.sh: line 7: syntax error near unexpected token `$'in\r''
'home/cmccabe/test.sh: line 7: `case "$id" in

This particular error means "Stop editing your scripts in Microsoft Notepad". Editing it in a Windows editor has filled them with carriage returns. To repair it:

Code:
tr -d '\r' < windowstext > unixtext

Why have you put absolutely everything in the case statement? Most of those statements will never be executed, since it jumps from ;; to esac. Not to mention, you can check for "end" in the same case statement. Try this:

Code:
printf "Is this a batch :"
while read id
do
        case "$id" in
        [yY]) echo perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo")' < file.txt 
                ;;
        [nN]) # code for X
                printf "Enter ID  : " ; read id
                [ -z "$id" ] && break
                [ "$id" = "end" ] && break
                echo perl table_annovar.pl ${id}_matched.avinput humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo
                ;;
        end)  break ;;
        *)     ;; # Unknown option, do nothing
        esac

        printf "Is this a batch :"
done


Last edited by Corona688; 10-23-2014 at 04:31 PM..
 

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shell(1F)							   FMLI Commands							 shell(1F)

NAME
shell - run a command using shell SYNOPSIS
shell command [command] ... DESCRIPTION
The shell function concatenate its arguments, separating each by a space, and passes this string to the shell ($SHELL if set, otherwise /usr/bin/sh). EXAMPLES
Example 1: A sample output of shell command. Since the Form and Menu Language does not directly support background processing, the shell function can be used instead. `shell "build prog > /dev/null &"` If you want the user to continue to be able to interact with the application while the background job is running, the output of an exe- cutable run by shell in the background must be redirected: to a file if you want to save the output, or to /dev/null if you don't want to save it (or if there is no output), otherwise your application may appear to be hung until the background job finishes processing. shell can also be used to execute a command that has the same name as an FMLI built-in function. NOTES
The arguments to shell will be concatenate using spaces, which may or may not do what is expected. The variables set in local environments will not be expanded by the shell because "local" means "local to the current process." ATTRIBUTES
See attributes(5) for descriptions of the following attributes: +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWcsu | +-----------------------------+-----------------------------+ SEE ALSO
sh(1), attributes(5) SunOS 5.10 5 Jul 1990 shell(1F)
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