11-06-2014
Perhaps you could simplify this and show us what you are trying to achieve for the call to bowtie and describe the inputs (file list etc.) and what you want it to end up calling it with. It is a little hard work to decipher your code without any design or comments and I worry about missing something vital.
Can you just explain the logic you use to get the bowtie calls?
Thanks, in advance,
Robin
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break(1) User Commands break(1)
NAME
break, continue - shell built-in functions to escape from or advance within a controlling while, for, foreach, or until loop
SYNOPSIS
sh
break [n]
continue [n]
csh
break
continue
ksh
*break [n]
*continue [n]
DESCRIPTION
sh
The break utility exits from the enclosing for or while loop, if any. If n is specified, break n levels.
The continue utility resumes the next iteration of the enclosing for or while loop. If n is specified, resume at the n-th enclosing loop.
csh
The break utility resumes execution after the end of the nearest enclosing foreach or while loop. The remaining commands on the current
line are executed. This allows multilevel breaks to be written as a list of break commands, all on one line.
The continue utility continues execution of the next iteration of the nearest enclosing while or foreach loop.
ksh
The break utility exits from the enclosed for, while, until, or select loop, if any. If n is specified, then break n levels. If n is
greater than the number of enclosing loops, the outermost enclosing loop shall be exited.
The continue utility resumes the next iteration of the enclosed for, while, until, or select loop. If n is specified then resume at the n-
th enclosed loop. If n is greater than the number of enclosing loops, the outermost enclosing loop shall be used.
On this man page, ksh(1) commands that are preceded by one or two * (asterisks) are treated specially in the following ways:
1. Variable assignment lists preceding the command remain in effect when the command completes.
2. I/O redirections are processed after variable assignments.
3. Errors cause a script that contains them to abort.
4. Words that follow a command preceded by ** that are in the format of a variable assignment are expanded with the same rules as a vari-
able assignment. This means that tilde substitution is performed after the = sign, and also that word splitting and file name genera-
tion are not performed.
ATTRIBUTES
See attributes(5) for descriptions of the following attributes:
+-----------------------------+-----------------------------+
| ATTRIBUTE TYPE | ATTRIBUTE VALUE |
+-----------------------------+-----------------------------+
|Availability |SUNWcsu |
+-----------------------------+-----------------------------+
SEE ALSO
csh(1), exit(1), ksh(1), sh( 1), attributes(5)
SunOS 5.10 17 Jul 2002 break(1)