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Full Discussion: variable issue in a bash in a shell script
Top Forums Shell Programming and Scripting variable issue in a bash in a shell script Post 302562732 by bioBob on Saturday 8th of October 2011 12:13:34 AM
Old 10-08-2011
variable issue in a bash in a shell script
Hi,

I am trying to write a PBS shell script that launches a bash process. The issue is that the bash process needs a variable in it and the shell script is interpreting the variable. How do I pass this as a literal string? Here is my code snippit:
Code:
TMP=".fasta"
FILEOUT=$FILE$TMP
cd ${PBS_O_WORKDIR}
bash "cat $FILE | perl -e '$i=0;while(<>){if(/^\@/&&$i==0){s/^\@/\>/;print;}elsif($i==1){print;$i=-3}$i++;}' > $FILEOUT"

The part that is giving the issues is the $i in the bash line. That is being interpreted and passed as a null string. I tried using /$i which gives the same result. My shell output looks like this:
Code:
bash: cat s_1_1.fastq | perl -e '=0;while(<>){if(/^\@/&&==0){s/^\@/\>/;print;}
elsif(==1){print;=-3}++;}' > s_1_1.fastq.fasta: No such file or directory

I am guessing there is another error in this because of the no such file part, but when I type
Code:
cat s_1_1.fastq | perl -e '$i=0;while(<>){if(/^\@/&&$i==0){s/^\@/\>/;print;}elsif($i==1){print;$i=-3}
$i++;}' > s_1_1.fastq.fasta

at the command prompt, it works.
Last edited by Scott; 10-08-2011 at 04:37 AM.. Reason: Please use code tags
 

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LEARN ABOUT DEBIAN

syslogout

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

NAME

       syslogout - modular centralized shell logout mechanism

DESCRIPTION

       syslogout is a generic approach to enable centralized shell logout actions for all users of a given system in a modular and centralized way
       mostly aimed at avoiding work for lazy sysadmins.  It has only been tested to work with the bash shell.

       It basically consists of the small /etc/syslogout shell script which invokes other small shell scripts having a .bash suffix which are con-
       tained  in  the	/etc/syslogout.d/ directory.  The system administrator can drop in any script he wants without any naming convention other
       than that the scripts need to have a .bash suffix to enable automagic sourcing by the /etc/syslogout script.

       For shell sessions, the contents of /etc/syslogout.d/" will be sourced by every user at logout if the following lines are  present  in  his
       $HOME/.bash_logout:

	   if [ -f /etc/syslogout ]; then
	       . /etc/syslogout
	   fi

       If  used  for X sessions it is advisable to include the former statement into the Xreset script of the X display manager instead to prevent
       that closing of an terminal emulator window yields unexpected results in your running X session if your X11 terminal emulator  is  using  a
       login  shell.   Be  sure  then to run it under the user-id of the X session's user.  See the example files in /usr/share/doc/syslogout/ for
       illustration.

       Users not wanting /etc/syslogout to be sourced for their environment can easily disable it's automatic mechanism.  It can  be  disabled	by
       simply creating an empty file called $HOME/.nosyslogout in the user's home directory using e.g. the touch(1) command.

       Any single configuration file in /etc/syslogout.d/ can simply be overridden by any user by creating a private $HOME/.syslogout.d/ directory
       which may contain a user's own version of any configuration file to be sourced instead of the system default.   It's  names  have  just	to
       match  exactly  the  system's  default /etc/syslogout.d/ configuration files.  Empty versions of these files contained in the $HOME/.syslo-
       gout.d/ directory automatically disable sourcing of the system wide version.

       Naturally, users can add and include their own private scripts to be automagically executed by /etc/syslogout at logout time.

OPTIONS

       There are no options other than those dictated by shell conventions.  Anything is defined within the configuration scripts themselves.

SEE ALSO

       The  README  files  and	configuration  examples  contained  in	/usr/share/doc/syslogout/  and	the  manual  page  for	bash(1),  xdm(1x),
       xdm.options(5), and wdm(1x).  Recommended further reading is everything related with shell programming.

       If  you need a similar mechanism for executing code at login time check out the related package sysprofile(8) which is a very close compan-
       ion to syslogout.

BUGS

       syslogout in its current form is mainly restricted to bash(1) syntax.  In fact it is actually  a rather embarrassing quick and  dirty  hack
       than  anything  else  -	but  it  works.   It  serves the practical need to enable a centralized bash configuration  until something better
       becomes available.  Your constructive criticism in making  this	into something better" is very welcome.  Before i forget to mention it: we
       take patches... ;-)

AUTHOR

       syslogout  was developed by Paul Seelig <pseelig@debian.org> specifically for the Debian GNU/Linux system.  Feel free to port it to and use
       it anywhere else under the conditions of either the GNU public license or the BSD license or both.  Better yet, please help to make it into
       something more worthwhile than it currently is.

																      SYSLOGOUT(8)
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