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Top Forums Shell Programming and Scripting Passing arguments to interactive program through bash script, here document Post 302909532 by Corona688 on Thursday 17th of July 2014 01:25:29 PM
Old 07-17-2014
Throwing which errors? Be specific.

Why are you putting the filename into data.txt ? To put it on the commandline, put it on the commandline.

Code:
/home/multalign/tab/ma filename < data.txt

Or if you meant you want the contents to be dynamic, don't store it in a file at all:

Code:
/home/multalign/tab/ma <<EOF
Text which can include ${VARIABLES}
EOF


Last edited by Corona688; 07-17-2014 at 02:30 PM..
 

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jrunscript(1)						      General Commands Manual						     jrunscript(1)

NAME
jrunscript - command line script shell SYNOPSIS
jrunscript [ options ] [ arguments... ] PARAMETERS
options Options, if used, should follow immediately after the command name. arguments Arguments, if used, should follow immediately after options or command name. DESCRIPTION
jrunscript is a command line script shell. jrunscript supports both an interactive (read-eval-print) mode and a batch (-f option) mode of script execution. This is a scripting language independent shell. By default, JavaScript is the language used, but the -l option can be used to specify a different language. Through Java to scripting language communication, jrunscript supports "exploratory programming" style. NOTE: This tool is experimental and may not be available in future versions of the JDK. OPTIONS
-classpath path Specify where to find the user's .class files that are accessed by the script. -cp path This is a synonym for -classpath path -Dname=value Set a Java system property. -Jflag Pass flag directly to the Java virtual machine on which jrunscript is run. -l language Use the specified scripting language. By default, JavaScript is used. Note that to use other scripting languages, you also need to spec- ify the corresponding script engine's jar file using -cp or -classpath option. -e script Evaluate the given script. This option can be used to run "one liner" scripts specified completely on the command line. -encoding encoding Specify the character encoding used while reading script files. -f script-file Evaluate the given script file (batch mode). -f - Read and evaluate a script from standard input (interactive mode). -help Output help message and exit. -? Output help message and exit. -q List all script engines available and exit. ARGUMENTS
If [arguments...] are present and if no -e or -f option is used, then the first argument is the script file and the rest of the arguments, if any, are passed as script arguments. If [arguments..] and -e or -f option are used, then all [arguments..] are passed as script argu- ments. If [arguments..], -e and -f are missing, interactive mode is used. Script arguments are available to a script in an engine variable named "arguments" of type String array. EXAMPLES
Executing inline scripts jrunscript -e "print('hello world')" jrunscript -e "cat('http://java.sun.com')" Use specified language and evaluate given script file jrunscript -l js -f test.js Interactive mode jrunscript js>print('hello world'); hello world js>34 + 55 89 js> thread(function() { print('hello world'); } hello world js> Run script file with script arguments jrunscript test.js arg1 arg2 arg3 test.js is script file to execute and arg1, arg2 and arg3 are passed to script as script arguments. Script can access these using "argu- ments" array. SEE ALSO
If JavaScript is used, then before evaluating any user defined script, jrunscript initializes certain built-in functions and objects. These JavaScript built-ins are documented in jsdocs. 06 Aug 2006 jrunscript(1)
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