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Top Forums Shell Programming and Scripting For loop to run external program Post 302557587 by oldmanwinter on Wednesday 21st of September 2011 04:18:33 PM
Old 09-21-2011
Question For loop to run external program

Hi, I was hoping for help with a for loop to run a program (vina) repeatedly using all the files in a folder as input. Currently my code looks like this:
Code:
#!/bin/bash
FILES=/home/afalk/Desktop/battest/*.pdbqt
for f in $FILES do
vina --config /home/afalk/Desktop/A.txt --ligand "$f".pdbqt
done

vina simply runs as "vina" in the terminal and this code is my attempt at translating a working batch file I had for windows. Whenever I try to run this, and after endless changes to the syntax all I get is "line 4: syntax error near unexpected token `vina'". Can anyone see what I'm doing wrong?
 

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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 /etc/smrsh, 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/procmail -f- /etc/procmailrcs/user || exit 75"'' Initial pathnames on programs are stripped, so forwarding to ``/usr/ucb/vacation'', ``/usr/bin/vacation'', ``/home/server/mydir/bin/vaca- tion'', and ``vacation'' all actually forward to ``/etc/smrsh/vacation''. System administrators should be conservative about populating the /etc/smrsh directory. Reasonable additions are vacation(1), procmail(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 /etc/smrsh directory. Note that this does not restrict the use of shell or perl scripts in the sm.bin directory (using the ``#!'' syntax); it simply disallows execution of arbitrary programs. FILES
/etc/smrsh - directory for restricted programs SEE ALSO
sendmail(8) $Date: 2002/04/25 13:33:40 $ SMRSH(8)
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