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Full Discussion: Bash while read line
Top Forums Shell Programming and Scripting Bash while read line Post 302910489 by chrisjorg on Thursday 24th of July 2014 07:44:14 PM
Old 07-24-2014
Bash while read line
I have a script batch_vmdgenpqr.sh which has a problem:


Code:
#!/bin/bash
while read line
do
      vmd.sh -dispdev text -e vmdgenpqr.tcl -args $line
done<file


The do line calls another program, VMD (called by vmd.sh) and it requires the values from $line, but this is not recognised by vmd. I'm not asking anyone to comment on VMD but is BASH passing on the correct variable?

Code:
[user]$ ./batch_vmdgenpqr.sh 
Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
Info) http://www.ks.uiuc.edu/Research/vmd/                         
Info) Email questions and bug reports to vmd@ks.uiuc.edu           
Info) Please include this reference in published work using VMD:   
Info)    Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual   
Info)    Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 32 CPUs detected.
Info) Free system memory: 126641MB (98%)
Info) Creating CUDA device pool and initializing hardware...
CUDA error: invalid device symbol, CUDAClearDevice.cu line 62
Info) Detected 1 available CUDA accelerator:
Info) [0] Quadro K5000        8 SM_3.0 @ 0.71 GHz, 4.0GB RAM, KTO, OIO, ZCP
Info) Dynamically loaded 2 plugins in directory:
Info) /opt/vmd-1.9.1/plugins/LINUXAMD64/molfile
can't read "line": no such variable

Last edited by Don Cragun; 07-24-2014 at 08:56 PM.. Reason: Add missing ending CODE tag.
 

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LEARN ABOUT DEBIAN

dpkg-www

DPKG-WWW(1)						      General Commands Manual						       DPKG-WWW(1)

NAME

       dpkg-www - program to remotely open a WWW Debian package browser

SYNOPSIS

       dpkg-www [-s|--stdout] [-h|--host host] [query]

DESCRIPTION

       dpkg-www is used to remotely control a WEB browser and open a dpkg URL on the local host from an interactive shell or script.

       If  the	command  is invoked while running under X-window the script will try to find an installed X browser to open the specified URL.	If
       not running under X it will try to use a text browser instead.

       If Netscape is found and a Netscape instance is already running it will be asked to open the dpkg URL on localhost with the optional  query
       supplied on the command line.  If there is no browser running, it will start automatically a new one.

       The  functionality  provided  by this program is identical to running a web browser with the -remote openURL(http://localhost/cgi-bin/dpkg)
       argument or opening the same URL from within the browser.

       dpkg-www-installer is an helper application which can configured in the WWW browser for	web  installation.  It	should	never  be  invoked
       directly by the user.

OPTIONS

       -s, --stdout
	      Redirect output to stdout. Requires one of the text browsers (lynx, lynx-ssl or links) installed.

       -h, --host host
	      Send the query to a remote host, where dpkg-www must be installed.

       query  Specifies  an  optional  package name, an absolute pathname or a query argument which is passed to the dpkg cgi-bin. See dpkg-www(8)
	      for more information about the use of the cgi.

FILES

       /etc/dpkg-www.conf

       ~/.dpkg-www
	      Configuration files for dpkg-www. It is not necessary for these files to exist, there are sensible defaults for everything, but  you
	      can specify your preferred www browser with the DPKG_WWW_BROWSER variable, for example: DPKG_WWW_BROWSER=mozilla

EXAMPLES

       dpkg-www
	      This would open a dpkg URL on localhost listing all the installed packages.

       dpkg-www bash
	      This would open a dpkg URL asking info on the bash package.

       dpkg-www -h pisolo bash
	      This would open a dpkg URL asking info on the bash package on host pisolo.

       dpkg-www 'dpkg*'
	      This would open a dpkg URL listing all packages matching dpkg*.

       dpkg-www /bin/bash
	      This would open a dpkg URL asking info on the package(s) owning the file /bin/bash .

       dpkg-www depends=svgalib
	      This would open a dpkg URL listing all packages depending on svgalib.

       dpkg-www --stdout depends=awk | grep ^ii
	      This would list on stdout all packages depending on awk and grep all lines of installed packages.

SEE ALSO

       dpkg(8), dpkg-www(8)

AUTHOR

       Massimo Dal Zotto <dz@debian.org>.
       Bugs should be reported via the normal Debian bug reporting system.

LICENCE

       dpkg-www is licensed under the GNU General Public License version 2.

								 September 1, 2004						       DPKG-WWW(1)
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