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Full Discussion: Change directory shell
Top Forums Shell Programming and Scripting Change directory shell Post 302922805 by cmccabe on Tuesday 28th of October 2014 11:28:20 AM
Old 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.txt

Code:
  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

Maybe:
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

Thanks Smilie.
Last edited by cmccabe; 10-28-2014 at 12:34 PM..
 

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LEARN ABOUT FREEBSD

smrsh

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

NAME

       smrsh - restricted shell for sendmail

SYNOPSIS

       smrsh -c command

DESCRIPTION

       The smrsh program is intended as a replacement for sh for use in the ``prog'' mailer in sendmail(8) configuration files.  It sharply limits
       the commands that can be run using the ``|program'' syntax of sendmail in order to improve the over all security of your system.   Briefly,
       even  if  a  ``bad guy'' can get sendmail to run a program without going through an alias or forward file, smrsh limits the set of programs
       that he or she can execute.

       Briefly, smrsh limits programs to be in a single directory, by default /usr/libexec/sm.bin, allowing the system administrator to choose the
       set  of	acceptable  commands,  and  to the shell builtin commands ``exec'', ``exit'', and ``echo''.  It also rejects any commands with the
       characters ``', `<', `>', `;', `$', `(', `)', `
' (carriage return), or `
' (newline) on the command line to prevent ``end run'' attacks.
       It allows ``||'' and ``&&'' to enable commands like: ``"|exec /usr/local/bin/filter || exit 75"''

       Initial	pathnames  on programs are stripped, so forwarding to ``/usr/bin/vacation'', ``/home/server/mydir/bin/vacation'', and ``vacation''
       all actually forward to ``/usr/libexec/sm.bin/vacation''.

       System administrators should be conservative about populating the sm.bin directory.  For example, a reasonable  additions  is  vacation(1),
       and  the  like.	No matter how brow-beaten you may be, never include any shell or shell-like program (such as perl(1)) in the sm.bin direc-
       tory.  Note that this does not restrict the use of shell or perl scripts in the sm.bin directory (using the ``#!'' syntax); it simply  dis-
       allows  execution  of  arbitrary  programs.   Also,  including mail filtering programs such as procmail(1) is a very bad idea.  procmail(1)
       allows users to run arbitrary programs in their procmailrc(5).

COMPILATION

       Compilation should be trivial on most systems.  You may need to use -DSMRSH_PATH="path" to adjust the default search  path  (defaults	to
       ``/bin:/usr/bin'') and/or -DSMRSH_CMDDIR="dir" to change the default program directory (defaults to ``/usr/libexec/sm.bin'').

FILES

       /usr/adm/sm.bin - default directory for restricted programs on most OSs

       /var/adm/sm.bin - directory for restricted programs on HP UX and Solaris

       /usr/libexec/sm.bin - directory for restricted programs on FreeBSD (>= 3.3) and DragonFly BSD

SEE ALSO

       sendmail(8)

							   $Date: 2013-11-22 20:52:00 $ 						  SMRSH(8)
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