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Shell Programming and Scripting
Change directory shell
Post 302922805 by cmccabe on Tuesday 28th of October 2014 11:28:20 AM
10-28-2014
Code:
#!/bin/bash
echo -n "Enter number of sanger patients : "; read id
cd 'C:\Users\cmccabe\Desktop\annovar'
perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo")' < file.txtCode:
bash ~/sanger.sh Enter number of sanger patients : 2 ': not a valid identifierline 2: read: `id : No such file or directoryne 3: cd: C:\Users\cmccabe\Desktop\annovar /home/cmccabe/sanger.sh: line 4: file.txt: No such file or directory
Code:
while true
do
printf "Enter ID : " ; read id
[ -z "$id" ] && break
cd 'C:\Users\cmccabe\Desktop\annovar'
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
done
.Last edited by cmccabe; 10-28-2014 at 12:34 PM..
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LEARN ABOUT OPENSOLARIS
shells
shells(4) File Formats shells(4) NAME
shells - shell database SYNOPSIS
/etc/shells DESCRIPTION
The shells file contains a list of the shells on the system. Applications use this file to determine whether a shell is valid. See getuser- shell(3C). For each shell a single line should be present, consisting of the shell's path, relative to root. A hash mark (#) indicates the beginning of a comment; subsequent characters up to the end of the line are not interpreted by the routines which search the file. Blank lines are also ignored. The following default shells are used by utilities: /bin/bash, /bin/csh, /bin/jsh, /bin/ksh, /bin/ksh93, /bin/pfcsh, /bin/pfksh, /bin/pfsh, /bin/sh, /bin/tcsh, /bin/zsh, /sbin/jsh, /sbin/sh, /usr/bin/bash, /usr/bin/csh, /usr/bin/jsh, /usr/bin/ksh, /usr/bin/ksh93, /usr/bin/pfcsh, /usr/bin/pfksh, /usr/bin/pfsh, and /usr/bin/sh, /usr/bin/tcsh, /usr/bin/zsh, and /usr/sfw/bin/zsh. /etc/shells overrides the default list. Invalid shells in /etc/shells could cause unexpected behavior, such as being unable to log in by way of ftp(1). FILES
/etc/shells list of shells on system SEE ALSO
vipw(1B), ftpd(1M), sendmail(1M), getusershell(3C), aliases(4) SunOS 5.11 20 Nov 2007 shells(4)