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Top Forums Shell Programming and Scripting Newbie wanting help with a script Post 302556456 by foyn on Sunday 18th of September 2011 03:37:02 PM
Old 09-18-2011
Newbie wanting help with a script

Hi

I am new to scripting and having trouble with an assignment. I have written this script:

Code:
#!/bin/bash

PATH=/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin

printf "\nWhat is the name of the input file?  "
read INPUT_FILE

if test ! -f ./$INPUT_FILE ; then
  printf "\nNo matching file name!!!  Aborting!!!\n\n"
  exit 192
fi

clustalw -align -INFILE=$INPUT_FILE -TYPE=DNA -OUTFILE=$INPUT_FILE_clustal.output -OUTPUT=PHYLIP

collapse1.5 $INPUT_FILE_clustal.output > $INPUT_FILE_collapse.output

seqret  -nofeature -sequence $INPUT_FILE_collapse.output -sformat1 phylip -snucleotide1 -nofirstonly -outseq $INPUT_FILE.nexus -osformat nexusnon -auto

rm -f *.output


But I get this error message in the terminal:


Code:
Foyn@Havard-Foyns-MacBook-Air:~/Desktop/Foyn_Miniproject_2_Part_1$ Miniproject_2_script 

What is the name of the input file?  Part_2_Seq.fasta
/Users/Foyn/UNIX_progs/bin/Miniproject_2_script: line 20: clustalw: command not found
/Users/Foyn/UNIX_progs/bin/Miniproject_2_script: line 24: collapse1.5: command not found
/Users/Foyn/UNIX_progs/bin/Miniproject_2_script: line 28: seqret: command not found


When I run the individual commands in the terminal on the other hand it seems to be working.

Is there anyone that knows what the problem is??

Last edited by pludi; 09-18-2011 at 06:41 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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